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17-77196230-A-G

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Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001143998.2(SEC14L1):ā€‹c.738A>Gā€‹(p.Arg246=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00321 in 1,614,038 control chromosomes in the GnomAD database, including 154 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā˜…).

Frequency

Genomes: š‘“ 0.017 ( 90 hom., cov: 32)
Exomes š‘“: 0.0017 ( 64 hom. )

Consequence

SEC14L1
NM_001143998.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.19
Variant links:
Genes affected
SEC14L1 (HGNC:10698): (SEC14 like lipid binding 1) The protein encoded by this gene belongs to the SEC14 cytosolic factor family. It has similarity to yeast SEC14 and to Japanese flying squid RALBP which suggests a possible role of the gene product in an intracellular transport system. Multiple alternatively spliced transcript variants have been found for this gene; some variants represent read-through transcripts that include exons from the upstream gene C17orf86. [provided by RefSeq, Feb 2011]

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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=-0.76).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-77196230-A-G is Benign according to our data. Variant chr17-77196230-A-G is described in ClinVar as [Benign]. Clinvar id is 781390.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=-1.19 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0585 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SEC14L1NM_001143998.2 linkuse as main transcriptc.738A>G p.Arg246= synonymous_variant 8/17 ENST00000436233.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SEC14L1ENST00000436233.9 linkuse as main transcriptc.738A>G p.Arg246= synonymous_variant 8/171 NM_001143998.2 Q92503-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0174
AC:
2654
AN:
152170
Hom.:
88
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0604
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00714
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000220
Gnomad OTH
AF:
0.0134
GnomAD3 exomes
AF:
0.00445
AC:
1119
AN:
251312
Hom.:
35
AF XY:
0.00311
AC XY:
422
AN XY:
135848
show subpopulations
Gnomad AFR exome
AF:
0.0606
Gnomad AMR exome
AF:
0.00304
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000132
Gnomad OTH exome
AF:
0.00212
GnomAD4 exome
AF:
0.00172
AC:
2511
AN:
1461750
Hom.:
64
Cov.:
30
AF XY:
0.00148
AC XY:
1075
AN XY:
727196
show subpopulations
Gnomad4 AFR exome
AF:
0.0599
Gnomad4 AMR exome
AF:
0.00320
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000696
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000120
Gnomad4 OTH exome
AF:
0.00353
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0175
AC:
2663
AN:
152288
Hom.:
90
Cov.:
32
AF XY:
0.0165
AC XY:
1230
AN XY:
74462
show subpopulations
Gnomad4 AFR
AF:
0.0604
Gnomad4 AMR
AF:
0.00713
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000220
Gnomad4 OTH
AF:
0.0132
Alfa
AF:
0.00926
Hom.:
21
Bravo
AF:
0.0201
Asia WGS
AF:
0.00318
AC:
11
AN:
3478
EpiCase
AF:
0.000218
EpiControl
AF:
0.000178

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 testingInvitaeJul 15, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
CADD
Benign
1.2
DANN
Benign
0.70
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs73998660; hg19: chr17-75192312; API