rs4769585

chr13-27976441-C-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 0.384 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.400

Alfa AF: 0.418 Hom.: 4854

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4769585; hg19: chr13-28550578;