rs17663983

Positions:

• chr7-76775924-C-T

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 0.0942 in 151,586 control chromosomes in the GnomAD database, including 922 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 0.094 (922 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0942 AC: 14268 AN: 151468 Hom.: 923 Cov.: 31

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0800

Gnomad EAS AF: 0.0998

Gnomad SAS AF: 0.0809

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0807

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

GnomAD4 genome AF: 0.0942 AC: 14273 AN: 151586 Hom.: 922 Cov.: 31 AF XY: 0.0992 AC XY: 7351 AN XY: 74076

Gnomad4 AFR AF: 0.0215

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0800

Gnomad4 EAS AF: 0.0995

Gnomad4 SAS AF: 0.0818

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0813

Alfa AF: 0.112 Hom.: 153

Bravo AF: 0.0792

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17663983; hg19: chr7-76405241;