rs2775256

Variant names:

• chr14-20065677-A-G
• rs2775256

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 0.323 in 152,100 control chromosomes in the GnomAD database, including 8,158 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 0.32 (8158 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.699
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49036 AN: 151982 Hom.: 8147 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.323 AC: 49085 AN: 152100 Hom.: 8158 Cov.: 32 AF XY: 0.326 AC XY: 24208 AN XY: 74356

African (AFR) AF: 0.292 AC: 12129 AN: 41484

American (AMR) AF: 0.360 AC: 5503 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1132 AN: 3472

East Asian (EAS) AF: 0.524 AC: 2704 AN: 5158

South Asian (SAS) AF: 0.523 AC: 2521 AN: 4818

European-Finnish (FIN) AF: 0.265 AC: 2796 AN: 10566

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21218 AN: 67998

Other (OTH) AF: 0.337 AC: 713 AN: 2114

Alfa AF: 0.309 Hom.: 962

Bravo AF: 0.328

Asia WGS AF: 0.521 AC: 1806 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.3
DANN	Benign	0.31
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs2775256; hg19: chr14-20533836;