chr14-20226443-T-G

Variant names:

• chr14-20226443-T-G
• rs1959344

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 0.402 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.353 AC: 14643 AN: 41440

American (AMR) AF: 0.353 AC: 5392 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1694 AN: 3468

East Asian (EAS) AF: 0.316 AC: 1636 AN: 5182

South Asian (SAS) AF: 0.423 AC: 2031 AN: 4800

European-Finnish (FIN) AF: 0.404 AC: 4266 AN: 10552

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29782 AN: 67964

Other (OTH) AF: 0.432 AC: 909 AN: 2104

Alfa AF: 0.429 Hom.: 44534

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1959344; hg19: chr14-20694602;