rs7642482

Variant names:

• chr3-77668605-A-G
• rs7642482

Your query was ambiguous. Multiple possible variants found:

• chr3-77668605-A-G
• chr3-77668605-A-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 0.12 in 152,272 control chromosomes in the GnomAD database, including 1,412 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 0.12 (1412 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.83
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.174 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: 0.120 AC: 18245 AN: 152154 Hom.: 1411 Cov.: 33

Gnomad AFR AF: 0.0285

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.120 AC: 18240 AN: 152272 Hom.: 1412 Cov.: 33 AF XY: 0.120 AC XY: 8935 AN XY: 74462

African (AFR) AF: 0.0285 AC: 1183 AN: 41572

American (AMR) AF: 0.102 AC: 1556 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3472

East Asian (EAS) AF: 0.133 AC: 691 AN: 5178

South Asian (SAS) AF: 0.184 AC: 889 AN: 4820

European-Finnish (FIN) AF: 0.133 AC: 1410 AN: 10610

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11563 AN: 68004

Other (OTH) AF: 0.124 AC: 261 AN: 2112

Alfa AF: 0.141 Hom.: 2993

Bravo AF: 0.109

Asia WGS AF: 0.159 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	17
DANN	Benign	0.65
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs7642482; hg19: chr3-77717756;