chr4-73733092-G-T

Position:

• chr4-73733092-G-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 0.46 in 151,346 control chromosomes in the GnomAD database, including 17,796 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 0.46 (17796 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 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: 0.460 AC: 69559 AN: 151230 Hom.: 17792 Cov.: 30

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.460 AC: 69587 AN: 151346 Hom.: 17796 Cov.: 30 AF XY: 0.467 AC XY: 34468 AN XY: 73812

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.478

Alfa AF: 0.521 Hom.: 9638

Bravo AF: 0.448

Asia WGS AF: 0.587 AC: 2040 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4694636; hg19: chr4-74598809;