rs17501080

Positions:

• chr7-81774380-A-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 0.103 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.81774380A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;