3-46913914-G-C

Variant names:

• chr3-46913914-G-C
• rs4682845

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 0.611 in 152,074 control chromosomes in the GnomAD database, including 28,611 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 0.61 (28611 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.642 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: 0.611 AC: 92858 AN: 151956 Hom.: 28576 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.611 AC: 92951 AN: 152074 Hom.: 28611 Cov.: 32 AF XY: 0.606 AC XY: 45075 AN XY: 74328

African (AFR) AF: 0.580 AC: 24047 AN: 41468

American (AMR) AF: 0.590 AC: 9022 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2143 AN: 3468

East Asian (EAS) AF: 0.459 AC: 2366 AN: 5158

South Asian (SAS) AF: 0.572 AC: 2749 AN: 4808

European-Finnish (FIN) AF: 0.642 AC: 6790 AN: 10582

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 44012 AN: 67984

Other (OTH) AF: 0.584 AC: 1234 AN: 2114

Alfa AF: 0.525 Hom.: 1555

Bravo AF: 0.603

Asia WGS AF: 0.579 AC: 2015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.66
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs4682845; hg19: chr3-46955404;