4-74347587-G-T

Position:

• chr4-74347587-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 0.342 in 151,742 control chromosomes in the GnomAD database, including 9,528 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 0.34 (9528 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.45 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: 0.342 AC: 51861 AN: 151624 Hom.: 9505 Cov.: 31

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.342 AC: 51943 AN: 151742 Hom.: 9528 Cov.: 31 AF XY: 0.348 AC XY: 25785 AN XY: 74136

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.314

Alfa AF: 0.309 Hom.: 947

Bravo AF: 0.354

Asia WGS AF: 0.473 AC: 1647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12646908; hg19: chr4-75213304;