rs1385477

chr3-155187951-T-G

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 0.75 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.895

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.734

Alfa AF: 0.736 Hom.: 10541

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1385477; hg19: chr3-154905740;