rs17763430

Variant names:

• chr17-66208623-G-A
• rs17763430

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 0.131 in 151,922 control chromosomes in the GnomAD database, including 1,491 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 0.13 (1491 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 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: 0.131 AC: 19888 AN: 151804 Hom.: 1492 Cov.: 31

Gnomad AFR AF: 0.0553

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0391

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.131 AC: 19885 AN: 151922 Hom.: 1491 Cov.: 31 AF XY: 0.130 AC XY: 9639 AN XY: 74236

African (AFR) AF: 0.0553 AC: 2292 AN: 41424

American (AMR) AF: 0.158 AC: 2405 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 724 AN: 3468

East Asian (EAS) AF: 0.0390 AC: 202 AN: 5176

South Asian (SAS) AF: 0.132 AC: 637 AN: 4818

European-Finnish (FIN) AF: 0.139 AC: 1463 AN: 10512

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11724 AN: 67958

Other (OTH) AF: 0.162 AC: 343 AN: 2112

Alfa AF: 0.159 Hom.: 1469

Bravo AF: 0.131

Asia WGS AF: 0.0960 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	13
DANN	Benign	0.91
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs17763430; hg19: chr17-64204741;