4-157448278-G-A

Position:

• chr4-157448278-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 0.554 in 151,930 control chromosomes in the GnomAD database, including 25,129 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 0.55 (25129 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 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: 0.553 AC: 83998 AN: 151812 Hom.: 25084 Cov.: 32

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.554 AC: 84099 AN: 151930 Hom.: 25129 Cov.: 32 AF XY: 0.550 AC XY: 40809 AN XY: 74246

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.533

Alfa AF: 0.514 Hom.: 2631

Bravo AF: 0.560

Asia WGS AF: 0.421 AC: 1462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6843849; hg19: chr4-158369430;