17-41741012-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.938

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.893

Gnomad4 FIN AF: 0.769

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.835

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6503659; hg19: chr17-39897264;