17-41741012-A-T

Variant names:

• chr17-41741012-A-T
• rs6503659

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 0.85 in 152,202 control chromosomes in the GnomAD database, including 55,235 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 0.85 (55235 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.873
• Publications: 23 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 (AFR) allele frequency at 95% confidence interval = 0.93 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: 0.850 AC: 129216 AN: 152084 Hom.: 55171 Cov.: 32

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.893

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.850 AC: 129340 AN: 152202 Hom.: 55235 Cov.: 32 AF XY: 0.850 AC XY: 63256 AN XY: 74394

African (AFR) AF: 0.938 AC: 38996 AN: 41562

American (AMR) AF: 0.821 AC: 12554 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2634 AN: 3470

East Asian (EAS) AF: 0.898 AC: 4634 AN: 5162

South Asian (SAS) AF: 0.893 AC: 4310 AN: 4824

European-Finnish (FIN) AF: 0.769 AC: 8148 AN: 10600

Middle Eastern (MID) AF: 0.774 AC: 226 AN: 292

European-Non Finnish (NFE) AF: 0.814 AC: 55318 AN: 67992

Other (OTH) AF: 0.835 AC: 1756 AN: 2104

Alfa AF: 0.735 Hom.: 2075

Bravo AF: 0.853

Asia WGS AF: 0.913 AC: 3175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.71
PhyloP100		-0.87
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6503659; hg19: chr17-39897264;