rs17271855

Variant names:

• chr19-5524710-C-T
• rs17271855

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 0.137 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0355 AC: 1470 AN: 41456

American (AMR) AF: 0.155 AC: 2369 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 633 AN: 3470

East Asian (EAS) AF: 0.135 AC: 697 AN: 5172

South Asian (SAS) AF: 0.217 AC: 1045 AN: 4818

European-Finnish (FIN) AF: 0.141 AC: 1492 AN: 10578

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.186 AC: 12611 AN: 67920

Other (OTH) AF: 0.143 AC: 303 AN: 2112

Alfa AF: 0.166 Hom.: 3212

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
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs17271855; hg19: chr19-5524721;