chr17-73155214-T-C

Variant names:

• chr17-73155214-T-C
• rs1037257

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 0.549 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.581

Alfa AF: 0.653 Hom.: 42603

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1037257; hg19: chr17-71151353;