rs629537

chr3-55456985-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;