4-74537057-T-C

Position:

• chr4-74537057-T-C

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 0.783 in 151,854 control chromosomes in the GnomAD database, including 47,070 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 0.78 (47070 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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: 0.783 AC: 118810 AN: 151736 Hom.: 47033 Cov.: 31

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.783 AC: 118901 AN: 151854 Hom.: 47070 Cov.: 31 AF XY: 0.789 AC XY: 58514 AN XY: 74196

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.791

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.755

Alfa AF: 0.764 Hom.: 5556

Bravo AF: 0.787

Asia WGS AF: 0.894 AC: 3105 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1494889; hg19: chr4-75402774;