rs7652849

Variant names:

• chr3-46907036-T-C
• rs7652849

Your query was ambiguous. Multiple possible variants found:

• chr3-46907036-T-C
• chr3-46907036-T-G

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 0.928 in 152,172 control chromosomes in the GnomAD database, including 65,732 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 0.93 (65732 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.928 AC: 141142 AN: 152054 Hom.: 65674 Cov.: 31

Gnomad AFR AF: 0.983

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.936

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.973

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.910

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

GnomAD4 genome AF: 0.928 AC: 141258 AN: 152172 Hom.: 65732 Cov.: 31 AF XY: 0.928 AC XY: 69047 AN XY: 74390

African (AFR) AF: 0.983 AC: 40807 AN: 41508

American (AMR) AF: 0.929 AC: 14218 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.936 AC: 3250 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5154 AN: 5156

South Asian (SAS) AF: 0.972 AC: 4691 AN: 4826

European-Finnish (FIN) AF: 0.879 AC: 9316 AN: 10602

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60876 AN: 67982

Other (OTH) AF: 0.911 AC: 1924 AN: 2112

Alfa AF: 0.910 Hom.: 42976

Bravo AF: 0.935

Asia WGS AF: 0.987 AC: 3432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.70
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs7652849; hg19: chr3-46948526;