rs17271855

Variant names:

• chr19-5524710-C-T
• rs17271855

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 0.137 in 151,970 control chromosomes in the GnomAD database, including 1,736 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 0.14 (1736 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.206 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: 0.137 AC: 20838 AN: 151852 Hom.: 1735 Cov.: 31

Gnomad AFR AF: 0.0356

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.137 AC: 20846 AN: 151970 Hom.: 1736 Cov.: 31 AF XY: 0.136 AC XY: 10112 AN XY: 74284

Gnomad4 AFR AF: 0.0355

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.143

Alfa AF: 0.176 Hom.: 2463

Bravo AF: 0.133

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17271855; hg19: chr19-5524721;