rs17663983

Variant names:

• chr7-76775924-C-T
• rs17663983

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 0.0942 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.0942 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

African (AFR) AF: 0.0215 AC: 889 AN: 41410

American (AMR) AF: 0.106 AC: 1614 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.0800 AC: 277 AN: 3464

East Asian (EAS) AF: 0.0995 AC: 513 AN: 5156

South Asian (SAS) AF: 0.0818 AC: 394 AN: 4816

European-Finnish (FIN) AF: 0.225 AC: 2367 AN: 10516

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.117 AC: 7917 AN: 67728

Other (OTH) AF: 0.0813 AC: 171 AN: 2104

Alfa AF: 0.108 Hom.: 153

Bravo AF: 0.0792

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.59
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs17663983; hg19: chr7-76405241;