rs3918358

Variant names:

• chr3-46352928-C-A
• rs3918358

Your query was ambiguous. Multiple possible variants found:

• chr3-46352928-C-A
• chr3-46352928-C-G
• chr3-46352928-C-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 0.68 in 152,086 control chromosomes in the GnomAD database, including 35,233 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 0.68 (35233 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 14 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 (NFE) allele frequency at 95% confidence interval = 0.685 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: 0.680 AC: 103374 AN: 151968 Hom.: 35193 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.680 AC: 103455 AN: 152086 Hom.: 35233 Cov.: 32 AF XY: 0.678 AC XY: 50405 AN XY: 74336

African (AFR) AF: 0.669 AC: 27730 AN: 41468

American (AMR) AF: 0.647 AC: 9885 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2537 AN: 3470

East Asian (EAS) AF: 0.688 AC: 3570 AN: 5190

South Asian (SAS) AF: 0.645 AC: 3110 AN: 4818

European-Finnish (FIN) AF: 0.710 AC: 7503 AN: 10562

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46899 AN: 67976

Other (OTH) AF: 0.666 AC: 1406 AN: 2112

Alfa AF: 0.651 Hom.: 2809

Bravo AF: 0.677

Asia WGS AF: 0.693 AC: 2411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.35
DANN	Benign	0.60
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs3918358; hg19: chr3-46394419;