14-20226443-T-G

Position:

• chr14-20226443-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 0.402 in 152,000 control chromosomes in the GnomAD database, including 12,608 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 0.40 (12608 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61016 AN: 151882 Hom.: 12591 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.402 AC: 61077 AN: 152000 Hom.: 12608 Cov.: 32 AF XY: 0.398 AC XY: 29577 AN XY: 74290

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.432

Alfa AF: 0.437 Hom.: 30042

Bravo AF: 0.394

Asia WGS AF: 0.370 AC: 1288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1959344; hg19: chr14-20694602;