rs7645716

Variant names:

• chr3-46295290-G-A
• rs7645716

Your query was ambiguous. Multiple possible variants found:

• chr3-46295290-G-A
• chr3-46295290-G-C

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 0.274 in 151,942 control chromosomes in the GnomAD database, including 6,169 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 0.27 (6169 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 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: 0.274 AC: 41562 AN: 151824 Hom.: 6148 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.274 AC: 41618 AN: 151942 Hom.: 6169 Cov.: 31 AF XY: 0.280 AC XY: 20761 AN XY: 74252

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.297

Alfa AF: 0.269 Hom.: 11767

Bravo AF: 0.277

Asia WGS AF: 0.488 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.64
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7645716; hg19: chr3-46336781;