rs1955851

chr14-25480071-G-T

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 0.591 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.626

Alfa AF: 0.661 Hom.: 30584

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

Splicing

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

Publications

LitVar

Other links and lift over

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