chr4-124494379-C-T

Variant names:

• chr4-124494379-C-T
• rs6534441

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 0.592 in 152,020 control chromosomes in the GnomAD database, including 28,479 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 (28479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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: 0.593 AC: 90006 AN: 151904 Hom.: 28465 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.592 AC: 90060 AN: 152020 Hom.: 28479 Cov.: 32 AF XY: 0.596 AC XY: 44250 AN XY: 74306

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.632

Alfa AF: 0.628 Hom.: 7052

Bravo AF: 0.592

Asia WGS AF: 0.731 AC: 2542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
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: rs6534441; hg19: chr4-125415534;