4-14163091-T-A

Position:

• chr4-14163091-T-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 0.678 in 151,860 control chromosomes in the GnomAD database, including 35,558 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 0.68 (35558 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 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: 0.678 AC: 102806 AN: 151742 Hom.: 35501 Cov.: 31

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.678 AC: 102921 AN: 151860 Hom.: 35558 Cov.: 31 AF XY: 0.682 AC XY: 50657 AN XY: 74230

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.600

Gnomad4 OTH AF: 0.678

Alfa AF: 0.648 Hom.: 4026

Bravo AF: 0.688

Asia WGS AF: 0.790 AC: 2747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6449004; hg19: chr4-14164715;