16-51140318-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002968.3(SALL1):c.1904C>T(p.Pro635Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00304 in 1,614,090 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002968.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00282 AC: 429AN: 152200Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00324 AC: 812AN: 250604Hom.: 5 AF XY: 0.00307 AC XY: 416AN XY: 135584
GnomAD4 exome AF: 0.00306 AC: 4478AN: 1461772Hom.: 27 Cov.: 53 AF XY: 0.00310 AC XY: 2251AN XY: 727192
GnomAD4 genome AF: 0.00282 AC: 429AN: 152318Hom.: 1 Cov.: 32 AF XY: 0.00294 AC XY: 219AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:2
SALL1: BP4, BS1, BS2 -
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SALL1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not specified Benign:1
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Townes syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at