chr14-98766512-T-A

Variant names:

• chr14-98766512-T-A
• rs1955897

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 0.555 in 152,056 control chromosomes in the GnomAD database, including 24,923 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 0.56 (24923 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84376 AN: 151936 Hom.: 24898 Cov.: 32

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.555 AC: 84449 AN: 152056 Hom.: 24923 Cov.: 32 AF XY: 0.553 AC XY: 41074 AN XY: 74290

African (AFR) AF: 0.757 AC: 31418 AN: 41494

American (AMR) AF: 0.630 AC: 9624 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1364 AN: 3464

East Asian (EAS) AF: 0.526 AC: 2715 AN: 5166

South Asian (SAS) AF: 0.568 AC: 2741 AN: 4822

European-Finnish (FIN) AF: 0.395 AC: 4162 AN: 10546

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30889 AN: 67978

Other (OTH) AF: 0.542 AC: 1143 AN: 2110

Alfa AF: 0.498 Hom.: 2500

Bravo AF: 0.582

Asia WGS AF: 0.567 AC: 1972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.66
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs1955897; hg19: chr14-99232849; COSMIC: COSV107181273;