rs7617456

chr3-133009059-G-A

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 0.358 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.368

Alfa AF: 0.400 Hom.: 12512

Bravo AF: 0.355

Asia WGS AF: 0.284 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	6.0
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

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