17-36092731-A-G

Variant names:

• chr17-36092731-A-G
• rs9972960

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 0.639 in 152,088 control chromosomes in the GnomAD database, including 31,215 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 0.64 (31215 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.24
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97143 AN: 151970 Hom.: 31181 Cov.: 33

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.639 AC: 97222 AN: 152088 Hom.: 31215 Cov.: 33 AF XY: 0.638 AC XY: 47404 AN XY: 74346

African (AFR) AF: 0.605 AC: 25092 AN: 41448

American (AMR) AF: 0.701 AC: 10713 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2093 AN: 3472

East Asian (EAS) AF: 0.822 AC: 4258 AN: 5182

South Asian (SAS) AF: 0.621 AC: 2998 AN: 4826

European-Finnish (FIN) AF: 0.623 AC: 6587 AN: 10576

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.636 AC: 43230 AN: 67994

Other (OTH) AF: 0.659 AC: 1391 AN: 2112

Alfa AF: 0.640 Hom.: 135673

Bravo AF: 0.650

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.43
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs9972960; hg19: chr17-34420079;