17-49981460-C-T

Variant names:

• chr17-49981460-C-T
• rs11654766

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 0.662 in 151,958 control chromosomes in the GnomAD database, including 37,435 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 0.66 (37435 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.818 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: 0.663 AC: 100632 AN: 151840 Hom.: 37434 Cov.: 31

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.662 AC: 100648 AN: 151958 Hom.: 37435 Cov.: 31 AF XY: 0.661 AC XY: 49064 AN XY: 74254

African (AFR) AF: 0.298 AC: 12331 AN: 41394

American (AMR) AF: 0.758 AC: 11572 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2914 AN: 3470

East Asian (EAS) AF: 0.705 AC: 3633 AN: 5154

South Asian (SAS) AF: 0.664 AC: 3193 AN: 4808

European-Finnish (FIN) AF: 0.812 AC: 8577 AN: 10568

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 56012 AN: 67976

Other (OTH) AF: 0.699 AC: 1472 AN: 2106

Alfa AF: 0.762 Hom.: 60706

Bravo AF: 0.644

Asia WGS AF: 0.626 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	4.4
DANN	Benign	0.81
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs11654766; hg19: chr17-48058824;