4-14039299-G-A

Position:

• chr4-14039299-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 0.522 in 135,010 control chromosomes in the GnomAD database, including 18,571 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 0.52 (18571 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 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: 0.523 AC: 70515 AN: 134950 Hom.: 18561 Cov.: 22

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.522 AC: 70539 AN: 135010 Hom.: 18571 Cov.: 22 AF XY: 0.528 AC XY: 34434 AN XY: 65178

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.533

Alfa AF: 0.491 Hom.: 7860

Bravo AF: 0.482

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.76
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6847349; hg19: chr4-14040923; COSMIC: COSV69990087;