4-73425201-C-T

Position:

• chr4-73425201-C-T

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 0.453 in 151,892 control chromosomes in the GnomAD database, including 15,850 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 0.45 (15850 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

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 (AMR) allele frequency at 95% confidence interval = 0.535 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: 0.452 AC: 68647 AN: 151774 Hom.: 15820 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.453 AC: 68735 AN: 151892 Hom.: 15850 Cov.: 32 AF XY: 0.457 AC XY: 33945 AN XY: 74236

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.490

Alfa AF: 0.322 Hom.: 940

Bravo AF: 0.460

Asia WGS AF: 0.510 AC: 1775 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	0.076
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28585480; hg19: chr4-74290918;