rs4745758

Variant names:

• chr10-74808499-C-T
• rs4745758

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 0.284 in 150,282 control chromosomes in the GnomAD database, including 10,778 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 0.28 (10778 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 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: 0.284 AC: 42698 AN: 150172 Hom.: 10761 Cov.: 29

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.0498

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.0994

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.284 AC: 42753 AN: 150282 Hom.: 10778 Cov.: 29 AF XY: 0.284 AC XY: 20788 AN XY: 73326

African (AFR) AF: 0.663 AC: 26838 AN: 40506

American (AMR) AF: 0.268 AC: 4028 AN: 15016

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 460 AN: 3454

East Asian (EAS) AF: 0.307 AC: 1560 AN: 5086

South Asian (SAS) AF: 0.418 AC: 1996 AN: 4772

European-Finnish (FIN) AF: 0.0498 AC: 515 AN: 10332

Middle Eastern (MID) AF: 0.248 AC: 72 AN: 290

European-Non Finnish (NFE) AF: 0.0994 AC: 6739 AN: 67822

Other (OTH) AF: 0.248 AC: 518 AN: 2092

Alfa AF: 0.181 Hom.: 2435

Bravo AF: 0.314

Asia WGS AF: 0.375 AC: 1303 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	6.9
DANN	Benign	0.48
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs4745758; hg19: chr10-76568257;