chr14-98012267-G-A

Variant names:

• chr14-98012267-G-A
• rs876188

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 0.664 in 151,860 control chromosomes in the GnomAD database, including 35,755 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 0.66 (35755 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.801 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: 0.665 AC: 100859 AN: 151740 Hom.: 35752 Cov.: 30

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.664 AC: 100884 AN: 151860 Hom.: 35755 Cov.: 30 AF XY: 0.657 AC XY: 48783 AN XY: 74220

African (AFR) AF: 0.432 AC: 17886 AN: 41362

American (AMR) AF: 0.698 AC: 10666 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2896 AN: 3466

East Asian (EAS) AF: 0.338 AC: 1735 AN: 5130

South Asian (SAS) AF: 0.686 AC: 3295 AN: 4804

European-Finnish (FIN) AF: 0.673 AC: 7105 AN: 10552

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.807 AC: 54822 AN: 67960

Other (OTH) AF: 0.693 AC: 1459 AN: 2104

Alfa AF: 0.763 Hom.: 175088

Bravo AF: 0.656

Asia WGS AF: 0.488 AC: 1702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.50
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs876188; hg19: chr14-98478604; COSMIC: COSV53418436;