chr17-71249594-T-C

Variant names:

• chr17-71249594-T-C
• rs2058005

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 0.66 in 152,082 control chromosomes in the GnomAD database, including 35,127 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 (35127 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.885
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.785 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: 0.661 AC: 100391 AN: 151966 Hom.: 35113 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.660 AC: 100438 AN: 152082 Hom.: 35127 Cov.: 32 AF XY: 0.666 AC XY: 49491 AN XY: 74340

African (AFR) AF: 0.409 AC: 16940 AN: 41458

American (AMR) AF: 0.700 AC: 10689 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2541 AN: 3472

East Asian (EAS) AF: 0.732 AC: 3792 AN: 5178

South Asian (SAS) AF: 0.806 AC: 3889 AN: 4826

European-Finnish (FIN) AF: 0.821 AC: 8690 AN: 10586

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.758 AC: 51506 AN: 67968

Other (OTH) AF: 0.664 AC: 1402 AN: 2112

Alfa AF: 0.737 Hom.: 37259

Bravo AF: 0.638

Asia WGS AF: 0.785 AC: 2727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	15
DANN	Benign	0.69
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs2058005; hg19: chr17-69245735;