chr14-49321339-G-A

Position:

• chr14-49321339-G-A

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 0.586 in 152,104 control chromosomes in the GnomAD database, including 27,141 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 0.59 (27141 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138

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 (EAS) allele frequency at 95% confidence interval = 0.964 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: 0.586 AC: 89114 AN: 151986 Hom.: 27129 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.586 AC: 89163 AN: 152104 Hom.: 27141 Cov.: 32 AF XY: 0.588 AC XY: 43733 AN XY: 74346

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.579

Alfa AF: 0.544 Hom.: 3931

Bravo AF: 0.581

Asia WGS AF: 0.829 AC: 2883 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	2.6
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11846868; hg19: chr14-49788057;