14-21131933-T-G

Variant names:

• chr14-21131933-T-G
• rs1243482

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 0.482 in 152,032 control chromosomes in the GnomAD database, including 18,410 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 0.48 (18410 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.09
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 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: 0.482 AC: 73262 AN: 151914 Hom.: 18380 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.482 AC: 73347 AN: 152032 Hom.: 18410 Cov.: 32 AF XY: 0.488 AC XY: 36273 AN XY: 74306

African (AFR) AF: 0.361 AC: 14962 AN: 41452

American (AMR) AF: 0.512 AC: 7828 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2256 AN: 3468

East Asian (EAS) AF: 0.736 AC: 3809 AN: 5176

South Asian (SAS) AF: 0.650 AC: 3127 AN: 4812

European-Finnish (FIN) AF: 0.518 AC: 5477 AN: 10564

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34386 AN: 67964

Other (OTH) AF: 0.500 AC: 1053 AN: 2108

Alfa AF: 0.348 Hom.: 915

Bravo AF: 0.473

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.28
DANN	Benign	0.24
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs1243482; hg19: chr14-21600092;