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GeneBe

16-51137172-G-A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_002968.3(SALL1):c.3915C>T(p.Asn1305=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000506 in 152096 control chromosomes in the gnomAD Genomes database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.00051 ( 1 hom., cov: 31)
Exomes 𝑓: 0.0013 ( 7 hom. )

Consequence

SALL1
NM_002968.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.0560

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
?
Variant 16-51137172-G-A is Benign according to our data. Variant chr16-51137172-G-A is described in ClinVar as [Benign]. Clinvar id is 287591.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.056 with no splicing effect.
BS1
?
Variant frequency is greater than expected. gnomad allele frequency = 0.000506 (77/152096) while in subpopulation SAS AF= 0.00851 (41/4820). AF 95% confidence interval is 0.00644. There are 1 homozygotes in gnomad. There are 52 alleles in male gnomad subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 77 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SALL1NM_002968.3 linkuse as main transcriptc.3915C>T p.Asn1305= synonymous_variant 3/3 ENST00000251020.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SALL1ENST00000251020.9 linkuse as main transcriptc.3915C>T p.Asn1305= synonymous_variant 3/31 NM_002968.3 P2Q9NSC2-1

Frequencies

GnomAD3 genomes
AF:
0.000506
AC:
77
AN:
152096
Hom.:
1
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000720
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00851
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000235
Gnomad OTH
AF:
0.00240
GnomAD3 exomes
AF:
0.00128
AC:
321
AN:
251476
Hom.:
7
AF XY:
0.00166
AC XY:
226
AN XY:
135920
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000520
Gnomad ASJ exome
AF:
0.000298
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00810
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000404
Gnomad OTH exome
AF:
0.000978
GnomAD4 exome
AF:
0.000790
AC:
1155
AN:
1461884
Hom.:
18
AF XY:
0.000996
AC XY:
724
AN XY:
727242
show subpopulations
Gnomad4 AFR exome
AF:
0.000329
Gnomad4 AMR exome
AF:
0.000537
Gnomad4 ASJ exome
AF:
0.000115
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00879
Gnomad4 FIN exome
AF:
0.0000374
Gnomad4 NFE exome
AF:
0.000249
Gnomad4 OTH exome
AF:
0.000861
Alfa
AF:
0.000294
Hom.:
0
Bravo
AF:
0.000314
Asia WGS
AF:
0.00404
AC:
14
AN:
3478
EpiCase
AF:
0.000600
EpiControl
AF:
0.000771

ClinVar

Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxJul 08, 2020This variant is associated with the following publications: (PMID: 16892410, 11102974, 10819639) -
Benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2023SALL1: BP4, BP7, BS1, BS2 -
not specified Benign:1
Benign, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)May 12, 2016- -
Townes syndrome Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 06, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
Cadd
Benign
3.1
Dann
Benign
0.92

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs140524372; hg19: chr16-51171083; COSMIC: COSV51756991; COSMIC: COSV51756991; API