17-27214252-A-C

Variant names:

• chr17-27214252-A-C
• rs4795519

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 0.429 in 151,992 control chromosomes in the GnomAD database, including 15,111 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 0.43 (15111 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65158 AN: 151874 Hom.: 15066 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.429 AC: 65267 AN: 151992 Hom.: 15111 Cov.: 32 AF XY: 0.430 AC XY: 31982 AN XY: 74300

African (AFR) AF: 0.609 AC: 25220 AN: 41428

American (AMR) AF: 0.447 AC: 6834 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1165 AN: 3472

East Asian (EAS) AF: 0.524 AC: 2709 AN: 5170

South Asian (SAS) AF: 0.384 AC: 1848 AN: 4818

European-Finnish (FIN) AF: 0.326 AC: 3451 AN: 10578

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22769 AN: 67940

Other (OTH) AF: 0.410 AC: 865 AN: 2110

Alfa AF: 0.345 Hom.: 9758

Bravo AF: 0.448

Asia WGS AF: 0.439 AC: 1525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.30
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4795519; hg19: chr17-25541278;