3-87608282-A-G

Variant names:

• chr3-87608282-A-G
• rs7646773

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 0.478 in 151,984 control chromosomes in the GnomAD database, including 19,939 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 0.48 (19939 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72586 AN: 151864 Hom.: 19894 Cov.: 32

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.478 AC: 72680 AN: 151984 Hom.: 19939 Cov.: 32 AF XY: 0.476 AC XY: 35377 AN XY: 74288

African (AFR) AF: 0.765 AC: 31710 AN: 41454

American (AMR) AF: 0.379 AC: 5796 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1248 AN: 3466

East Asian (EAS) AF: 0.502 AC: 2582 AN: 5142

South Asian (SAS) AF: 0.319 AC: 1535 AN: 4816

European-Finnish (FIN) AF: 0.365 AC: 3856 AN: 10558

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24479 AN: 67962

Other (OTH) AF: 0.465 AC: 982 AN: 2112

Alfa AF: 0.395 Hom.: 53869

Bravo AF: 0.494

Asia WGS AF: 0.415 AC: 1444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.47
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7646773; hg19: chr3-87657432;