rs4769585

Variant names:

• chr13-27976441-C-T
• rs4769585

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 0.384 in 152,182 control chromosomes in the GnomAD database, including 12,350 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 0.38 (12350 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 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: 0.384 AC: 58349 AN: 152064 Hom.: 12344 Cov.: 34

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.384 AC: 58390 AN: 152182 Hom.: 12350 Cov.: 34 AF XY: 0.383 AC XY: 28502 AN XY: 74390

African (AFR) AF: 0.221 AC: 9194 AN: 41530

American (AMR) AF: 0.462 AC: 7061 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1474 AN: 3470

East Asian (EAS) AF: 0.191 AC: 988 AN: 5182

South Asian (SAS) AF: 0.254 AC: 1228 AN: 4830

European-Finnish (FIN) AF: 0.489 AC: 5178 AN: 10580

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31634 AN: 67982

Other (OTH) AF: 0.400 AC: 845 AN: 2114

Alfa AF: 0.420 Hom.: 6031

Bravo AF: 0.378

Asia WGS AF: 0.215 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.55
PhyloP100		0.093

Splicing

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

Other links and lift over

dbSNP: rs4769585; hg19: chr13-28550578;