chr17-66258441-A-G

Variant names:

• chr17-66258441-A-G
• rs10491174

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 0.127 in 152,248 control chromosomes in the GnomAD database, including 1,383 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 (1383 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.183 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: 0.127 AC: 19338 AN: 152130 Hom.: 1381 Cov.: 31

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.0917

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.127 AC: 19362 AN: 152248 Hom.: 1383 Cov.: 31 AF XY: 0.129 AC XY: 9607 AN XY: 74458

African (AFR) AF: 0.125 AC: 5195 AN: 41554

American (AMR) AF: 0.189 AC: 2880 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0917 AC: 318 AN: 3468

East Asian (EAS) AF: 0.100 AC: 518 AN: 5176

South Asian (SAS) AF: 0.107 AC: 514 AN: 4824

European-Finnish (FIN) AF: 0.130 AC: 1385 AN: 10614

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8131 AN: 68014

Other (OTH) AF: 0.123 AC: 260 AN: 2114

Alfa AF: 0.117 Hom.: 970

Bravo AF: 0.129

Asia WGS AF: 0.118 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.56
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs10491174; hg19: chr17-64254559;