chr14-100693079-T-G

Position:

• chr14-100693079-T-G

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 0.619 in 152,124 control chromosomes in the GnomAD database, including 30,540 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 0.62 (30540 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.718 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: 0.619 AC: 94114 AN: 152006 Hom.: 30513 Cov.: 33

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.619 AC: 94177 AN: 152124 Hom.: 30540 Cov.: 33 AF XY: 0.615 AC XY: 45752 AN XY: 74370

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.644

Alfa AF: 0.630 Hom.: 3023

Bravo AF: 0.617

Asia WGS AF: 0.543 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.80
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7149242; hg19: chr14-101159416; COSMIC: COSV68250653;