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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.120 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

Gnomad4 AFR AF: 0.0285

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.124

Alfa AF: 0.112 Hom.: 320

Bravo AF: 0.109

Asia WGS AF: 0.159 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7642482; hg19: chr3-77717756;