rs2256605

Variant names:

• chr14-61674004-C-G
• rs2256605

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 0.709 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.709 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

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.826

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.952

Gnomad4 NFE AF: 0.903

Gnomad4 OTH AF: 0.733

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2256605; hg19: chr14-62140722;