17-76848535-C-T

Variant names:

• chr17-76848535-C-T
• rs563079

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 0.124 in 152,010 control chromosomes in the GnomAD database, including 1,467 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 0.12 (1467 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18895 AN: 151892 Hom.: 1468 Cov.: 31

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0901

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0401

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0819

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0883

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.124 AC: 18912 AN: 152010 Hom.: 1467 Cov.: 31 AF XY: 0.123 AC XY: 9171 AN XY: 74330

African (AFR) AF: 0.217 AC: 9008 AN: 41420

American (AMR) AF: 0.0899 AC: 1372 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3468

East Asian (EAS) AF: 0.0402 AC: 208 AN: 5178

South Asian (SAS) AF: 0.134 AC: 644 AN: 4810

European-Finnish (FIN) AF: 0.0819 AC: 867 AN: 10580

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0883 AC: 6003 AN: 67984

Other (OTH) AF: 0.137 AC: 289 AN: 2110

Alfa AF: 0.0974 Hom.: 1428

Bravo AF: 0.129

Asia WGS AF: 0.0860 AC: 300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.60
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs563079; hg19: chr17-74844617;