rs275358

Variant names:

• chr3-81419762-A-C
• rs275358

Your query was ambiguous. Multiple possible variants found:

• chr3-81419762-A-C
• chr3-81419762-A-G
• chr3-81419762-A-T

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 0.569 in 151,882 control chromosomes in the GnomAD database, including 25,374 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 0.57 (25374 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.701 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: 0.569 AC: 86423 AN: 151764 Hom.: 25343 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.692

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.569 AC: 86490 AN: 151882 Hom.: 25374 Cov.: 32 AF XY: 0.572 AC XY: 42484 AN XY: 74256

African (AFR) AF: 0.446 AC: 18463 AN: 41426

American (AMR) AF: 0.606 AC: 9246 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2653 AN: 3464

East Asian (EAS) AF: 0.371 AC: 1913 AN: 5158

South Asian (SAS) AF: 0.721 AC: 3478 AN: 4826

European-Finnish (FIN) AF: 0.604 AC: 6372 AN: 10544

Middle Eastern (MID) AF: 0.697 AC: 202 AN: 290

European-Non Finnish (NFE) AF: 0.623 AC: 42280 AN: 67902

Other (OTH) AF: 0.605 AC: 1274 AN: 2106

Alfa AF: 0.580 Hom.: 24015

Bravo AF: 0.557

Asia WGS AF: 0.566 AC: 1965 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.45
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs275358; hg19: chr3-81468913;