chr4-73990818-C-T

Variant names:

• chr4-73990818-C-T
• rs2457996

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 0.82 in 151,972 control chromosomes in the GnomAD database, including 52,338 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 0.82 (52338 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 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: 0.821 AC: 124627 AN: 151854 Hom.: 52339 Cov.: 30

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.907

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.820 AC: 124659 AN: 151972 Hom.: 52338 Cov.: 30 AF XY: 0.824 AC XY: 61240 AN XY: 74302

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.907

Gnomad4 ASJ AF: 0.876

Gnomad4 EAS AF: 0.966

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.891

Gnomad4 OTH AF: 0.835

Alfa AF: 0.878 Hom.: 26731

Bravo AF: 0.812

Asia WGS AF: 0.876 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2457996; hg19: chr4-74856535;