4-74537057-T-C

Variant names:

• chr4-74537057-T-C
• rs1494889

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 0.783 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
• Publications: 1 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.853 AC: 35368 AN: 41476

American (AMR) AF: 0.807 AC: 12274 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2025 AN: 3466

East Asian (EAS) AF: 0.987 AC: 5095 AN: 5162

South Asian (SAS) AF: 0.791 AC: 3814 AN: 4822

European-Finnish (FIN) AF: 0.821 AC: 8658 AN: 10550

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49385 AN: 67856

Other (OTH) AF: 0.755 AC: 1594 AN: 2110

Alfa AF: 0.767 Hom.: 5839

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1494889; hg19: chr4-75402774;