rs275711

Variant names:

• chr3-148656844-A-G
• rs275711

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 0.774 in 150,216 control chromosomes in the GnomAD database, including 45,140 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 0.77 (45140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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 (EAS) allele frequency at 95% confidence interval = 0.892 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: 0.774 AC: 116227 AN: 150100 Hom.: 45095 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.914

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.774 AC: 116328 AN: 150216 Hom.: 45140 Cov.: 32 AF XY: 0.776 AC XY: 57005 AN XY: 73476

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.851

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.914

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.791

Alfa AF: 0.791 Hom.: 9747

Bravo AF: 0.778

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs275711; hg19: chr3-148374631;