17-73155214-T-C

Variant names:

• chr17-73155214-T-C
• rs1037257

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 0.549 in 152,112 control chromosomes in the GnomAD database, including 25,916 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 0.55 (25916 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 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: 0.550 AC: 83546 AN: 151994 Hom.: 25916 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.549 AC: 83561 AN: 152112 Hom.: 25916 Cov.: 32 AF XY: 0.548 AC XY: 40760 AN XY: 74344

African (AFR) AF: 0.238 AC: 9886 AN: 41522

American (AMR) AF: 0.622 AC: 9503 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2330 AN: 3466

East Asian (EAS) AF: 0.796 AC: 4107 AN: 5160

South Asian (SAS) AF: 0.660 AC: 3177 AN: 4814

European-Finnish (FIN) AF: 0.590 AC: 6247 AN: 10584

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46180 AN: 67964

Other (OTH) AF: 0.581 AC: 1229 AN: 2116

Alfa AF: 0.640 Hom.: 52609

Bravo AF: 0.537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.4
DANN	Benign	0.73
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs1037257; hg19: chr17-71151353;