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GeneBe

1-169708538-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_000655.5(SELL):c.351T>C(p.Gly117=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00241 in 1,613,418 control chromosomes in the GnomAD database, including 81 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.013 ( 35 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 46 hom. )

Consequence

SELL
NM_000655.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.08
Variant links:
Genes affected
SELL (HGNC:10720): (selectin L) This gene encodes a cell surface adhesion molecule that belongs to a family of adhesion/homing receptors. The encoded protein contains a C-type lectin-like domain, a calcium-binding epidermal growth factor-like domain, and two short complement-like repeats. The gene product is required for binding and subsequent rolling of leucocytes on endothelial cells, facilitating their migration into secondary lymphoid organs and inflammation sites. Single-nucleotide polymorphisms in this gene have been associated with various diseases including immunoglobulin A nephropathy. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Oct 2009]
FIRRM (HGNC:25565): (FIGNL1 interacting regulator of recombination and mitosis)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-169708538-A-G is Benign according to our data. Variant chr1-169708538-A-G is described in ClinVar as [Benign]. Clinvar id is 789697.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-2.08 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0126 (1920/152160) while in subpopulation AFR AF= 0.0433 (1797/41510). AF 95% confidence interval is 0.0416. There are 35 homozygotes in gnomad4. There are 909 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 35 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SELLNM_000655.5 linkuse as main transcriptc.351T>C p.Gly117= synonymous_variant 3/9 ENST00000236147.6
SELLNR_029467.2 linkuse as main transcriptn.320T>C non_coding_transcript_exon_variant 1/7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SELLENST00000236147.6 linkuse as main transcriptc.351T>C p.Gly117= synonymous_variant 3/91 NM_000655.5 P1P14151-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0125
AC:
1905
AN:
152042
Hom.:
35
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0431
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00597
Gnomad ASJ
AF:
0.000864
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.0115
GnomAD3 exomes
AF:
0.00314
AC:
781
AN:
248502
Hom.:
12
AF XY:
0.00234
AC XY:
316
AN XY:
134810
show subpopulations
Gnomad AFR exome
AF:
0.0447
Gnomad AMR exome
AF:
0.00192
Gnomad ASJ exome
AF:
0.000199
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000163
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000444
Gnomad OTH exome
AF:
0.00183
GnomAD4 exome
AF:
0.00135
AC:
1970
AN:
1461258
Hom.:
46
Cov.:
31
AF XY:
0.00110
AC XY:
802
AN XY:
726916
show subpopulations
Gnomad4 AFR exome
AF:
0.0478
Gnomad4 AMR exome
AF:
0.00256
Gnomad4 ASJ exome
AF:
0.000153
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000197
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000252
Gnomad4 OTH exome
AF:
0.00333
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0126
AC:
1920
AN:
152160
Hom.:
35
Cov.:
32
AF XY:
0.0122
AC XY:
909
AN XY:
74376
show subpopulations
Gnomad4 AFR
AF:
0.0433
Gnomad4 AMR
AF:
0.00596
Gnomad4 ASJ
AF:
0.000864
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.0114
Alfa
AF:
0.00627
Hom.:
9
Bravo
AF:
0.0149
Asia WGS
AF:
0.00346
AC:
12
AN:
3478
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
Cadd
Benign
7.6
Dann
Benign
0.68

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4987286; hg19: chr1-169677679; API