rs17501080

Variant names:

• chr7-81774380-A-C
• rs17501080

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 0.103 in 152,036 control chromosomes in the GnomAD database, including 849 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 0.10 (849 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 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: 0.103 AC: 15719 AN: 151918 Hom.: 848 Cov.: 32

Gnomad AFR AF: 0.0975

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.00945

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0809

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

GnomAD4 genome AF: 0.103 AC: 15727 AN: 152036 Hom.: 849 Cov.: 32 AF XY: 0.104 AC XY: 7710 AN XY: 74316

Gnomad4 AFR AF: 0.0974

Gnomad4 AMR AF: 0.0695

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.00947

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0801

Alfa AF: 0.122 Hom.: 147

Bravo AF: 0.0955

Asia WGS AF: 0.0660 AC: 233 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.9
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17501080; hg19: chr7-81403696;