rs7617456

Variant names:

• chr3-133009059-G-A
• rs7617456

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 0.358 in 152,122 control chromosomes in the GnomAD database, including 10,295 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 0.36 (10295 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.585
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.441 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: 0.358 AC: 54380 AN: 152006 Hom.: 10281 Cov.: 33

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.358 AC: 54416 AN: 152122 Hom.: 10295 Cov.: 33 AF XY: 0.358 AC XY: 26587 AN XY: 74360

African (AFR) AF: 0.232 AC: 9618 AN: 41478

American (AMR) AF: 0.450 AC: 6874 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1348 AN: 3470

East Asian (EAS) AF: 0.238 AC: 1233 AN: 5176

South Asian (SAS) AF: 0.355 AC: 1710 AN: 4820

European-Finnish (FIN) AF: 0.394 AC: 4173 AN: 10592

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28234 AN: 67974

Other (OTH) AF: 0.368 AC: 777 AN: 2114

Alfa AF: 0.393 Hom.: 35541

Bravo AF: 0.355

Asia WGS AF: 0.284 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.70
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs7617456; hg19: chr3-132727903; COSMIC: COSV60112977;