rs1955851

Variant names:

• chr14-25480071-G-T
• rs1955851

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 0.591 in 152,010 control chromosomes in the GnomAD database, including 28,038 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 0.59 (28038 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.74 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: 0.592 AC: 89851 AN: 151892 Hom.: 28023 Cov.: 33

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.591 AC: 89905 AN: 152010 Hom.: 28038 Cov.: 33 AF XY: 0.593 AC XY: 44056 AN XY: 74300

African (AFR) AF: 0.385 AC: 15960 AN: 41436

American (AMR) AF: 0.663 AC: 10116 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1940 AN: 3468

East Asian (EAS) AF: 0.759 AC: 3923 AN: 5166

South Asian (SAS) AF: 0.667 AC: 3219 AN: 4826

European-Finnish (FIN) AF: 0.609 AC: 6432 AN: 10562

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46308 AN: 67984

Other (OTH) AF: 0.626 AC: 1319 AN: 2108

Alfa AF: 0.659 Hom.: 35362

Bravo AF: 0.588

Asia WGS AF: 0.701 AC: 2436 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.33
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1955851; hg19: chr14-25949277; COSMIC: COSV66931234;