17-41094387-C-T

Variant names:

• chr17-41094387-C-T
• rs4006360

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 0.621 in 151,986 control chromosomes in the GnomAD database, including 29,490 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 0.62 (29490 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 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: 0.621 AC: 94241 AN: 151868 Hom.: 29462 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.621 AC: 94310 AN: 151986 Hom.: 29490 Cov.: 32 AF XY: 0.619 AC XY: 45979 AN XY: 74266

African (AFR) AF: 0.637 AC: 26408 AN: 41442

American (AMR) AF: 0.611 AC: 9338 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2250 AN: 3472

East Asian (EAS) AF: 0.422 AC: 2174 AN: 5146

South Asian (SAS) AF: 0.498 AC: 2400 AN: 4818

European-Finnish (FIN) AF: 0.662 AC: 6978 AN: 10548

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42650 AN: 67960

Other (OTH) AF: 0.631 AC: 1333 AN: 2114

Alfa AF: 0.619 Hom.: 10564

Bravo AF: 0.617

Asia WGS AF: 0.500 AC: 1743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.8
DANN	Benign	0.10
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs4006360; hg19: chr17-39250639;