4-73425201-C-T

Variant names:

• chr4-73425201-C-T
• rs28585480

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.461 AC: 19118 AN: 41426

American (AMR) AF: 0.545 AC: 8325 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1931 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2291 AN: 5140

South Asian (SAS) AF: 0.480 AC: 2309 AN: 4812

European-Finnish (FIN) AF: 0.455 AC: 4794 AN: 10544

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28401 AN: 67924

Other (OTH) AF: 0.490 AC: 1033 AN: 2110

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs28585480; hg19: chr4-74290918;