rs2256605

Variant names:

• chr14-61674004-C-G
• rs2256605

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 0.709 in 152,222 control chromosomes in the GnomAD database, including 44,517 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 0.71 (44517 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107889 AN: 152104 Hom.: 44511 Cov.: 33

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.709 AC: 107927 AN: 152222 Hom.: 44517 Cov.: 33 AF XY: 0.716 AC XY: 53271 AN XY: 74440

African (AFR) AF: 0.251 AC: 10400 AN: 41488

American (AMR) AF: 0.826 AC: 12645 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2775 AN: 3472

East Asian (EAS) AF: 0.825 AC: 4282 AN: 5188

South Asian (SAS) AF: 0.775 AC: 3737 AN: 4820

European-Finnish (FIN) AF: 0.952 AC: 10106 AN: 10612

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.903 AC: 61398 AN: 68024

Other (OTH) AF: 0.733 AC: 1549 AN: 2112

Alfa AF: 0.790 Hom.: 6451

Bravo AF: 0.682

Asia WGS AF: 0.782 AC: 2718 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.1
DANN	Benign	0.79
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs2256605; hg19: chr14-62140722;