3-46507698-A-C

Variant names:

• chr3-46507698-A-C
• rs7371865

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 0.95 in 152,302 control chromosomes in the GnomAD database, including 68,870 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 0.95 (68870 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.950 AC: 144633 AN: 152184 Hom.: 68809 Cov.: 32

Gnomad AFR AF: 0.986

Gnomad AMI AF: 0.951

Gnomad AMR AF: 0.965

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.994

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.958

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

GnomAD4 genome AF: 0.950 AC: 144753 AN: 152302 Hom.: 68870 Cov.: 32 AF XY: 0.951 AC XY: 70841 AN XY: 74466

African (AFR) AF: 0.986 AC: 41009 AN: 41574

American (AMR) AF: 0.965 AC: 14768 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 3404 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5177 AN: 5178

South Asian (SAS) AF: 0.994 AC: 4798 AN: 4828

European-Finnish (FIN) AF: 0.923 AC: 9793 AN: 10608

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.921 AC: 62622 AN: 68028

Other (OTH) AF: 0.958 AC: 2024 AN: 2112

Alfa AF: 0.937 Hom.: 119276

Bravo AF: 0.955

Asia WGS AF: 0.996 AC: 3463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.79
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7371865; hg19: chr3-46549188;