rs629537

Variant names:

• chr3-55456985-G-A
• rs629537

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.156 in 152,156 control chromosomes in the GnomAD database, including 2,110 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2110 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23750 AN: 152038 Hom.: 2107 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.0721

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0957

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.165

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.156 AC: 23774 AN: 152156 Hom.: 2110 Cov.: 33 AF XY: 0.152 AC XY: 11290 AN XY: 74408

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.0720

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.0957

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.163

Alfa AF: 0.140 Hom.: 1623

Bravo AF: 0.163

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs629537; hg19: chr3-55491013;