rs1385477

Variant names:

• chr3-155187951-T-G
• rs1385477

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.75 in 152,090 control chromosomes in the GnomAD database, including 43,449 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 0.75 (43449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.887 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: 0.750 AC: 113918 AN: 151972 Hom.: 43396 Cov.: 32

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.750 AC: 114030 AN: 152090 Hom.: 43449 Cov.: 32 AF XY: 0.745 AC XY: 55365 AN XY: 74332

African (AFR) AF: 0.895 AC: 37148 AN: 41522

American (AMR) AF: 0.710 AC: 10845 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2309 AN: 3472

East Asian (EAS) AF: 0.697 AC: 3591 AN: 5154

South Asian (SAS) AF: 0.627 AC: 3032 AN: 4832

European-Finnish (FIN) AF: 0.656 AC: 6922 AN: 10556

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47631 AN: 67968

Other (OTH) AF: 0.734 AC: 1549 AN: 2110

Alfa AF: 0.733 Hom.: 17184

Bravo AF: 0.764

Asia WGS AF: 0.685 AC: 2381 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.71
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs1385477; hg19: chr3-154905740;