17-73161126-G-T

Variant names:

• chr17-73161126-G-T
• rs1037260

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 0.88 in 152,092 control chromosomes in the GnomAD database, including 59,629 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 0.88 (59629 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.997
• Publications: 7 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 (NFE) allele frequency at 95% confidence interval = 0.947 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: 0.880 AC: 133765 AN: 151974 Hom.: 59600 Cov.: 30

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.941

Gnomad FIN AF: 0.957

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.880 AC: 133853 AN: 152092 Hom.: 59629 Cov.: 30 AF XY: 0.881 AC XY: 65470 AN XY: 74344

African (AFR) AF: 0.728 AC: 30179 AN: 41432

American (AMR) AF: 0.875 AC: 13369 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.942 AC: 3272 AN: 3472

East Asian (EAS) AF: 0.881 AC: 4557 AN: 5170

South Asian (SAS) AF: 0.942 AC: 4531 AN: 4812

European-Finnish (FIN) AF: 0.957 AC: 10137 AN: 10596

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.953 AC: 64805 AN: 68010

Other (OTH) AF: 0.873 AC: 1844 AN: 2112

Alfa AF: 0.917 Hom.: 130691

Bravo AF: 0.867

Asia WGS AF: 0.884 AC: 3073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.69
DANN	Benign	0.73
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1037260; hg19: chr17-71157265;