rs876188

chr14-98012267-G-Achr14-98012267-G-C

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 0.664 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.693

Alfa AF: 0.785 Hom.: 87532

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

Splicing

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

Publications

LitVar

Other links and lift over

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