17-49987926-A-T

Variant names:

• chr17-49987926-A-T
• rs11871663

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 0.536 in 151,808 control chromosomes in the GnomAD database, including 22,105 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 0.54 (22105 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.489
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 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: 0.536 AC: 81377 AN: 151690 Hom.: 22096 Cov.: 31

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.536 AC: 81426 AN: 151808 Hom.: 22105 Cov.: 31 AF XY: 0.543 AC XY: 40296 AN XY: 74182

African (AFR) AF: 0.537 AC: 22211 AN: 41388

American (AMR) AF: 0.539 AC: 8232 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2140 AN: 3468

East Asian (EAS) AF: 0.792 AC: 4049 AN: 5112

South Asian (SAS) AF: 0.631 AC: 3024 AN: 4794

European-Finnish (FIN) AF: 0.546 AC: 5772 AN: 10574

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34095 AN: 67880

Other (OTH) AF: 0.551 AC: 1161 AN: 2108

Alfa AF: 0.504 Hom.: 2361

Bravo AF: 0.539

Asia WGS AF: 0.703 AC: 2444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	14
DANN	Benign	0.57
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs11871663; hg19: chr17-48065290;