rs6577059

chr13-113646377-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 0.163 in 152,112 control chromosomes in the GnomAD database, including 2,598 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 0.16 (2598 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 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: 0.163 AC: 24746 AN: 151994 Hom.: 2595 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0532

Gnomad SAS AF: 0.0672

Gnomad FIN AF: 0.0692

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.163 AC: 24779 AN: 152112 Hom.: 2598 Cov.: 32 AF XY: 0.157 AC XY: 11683 AN XY: 74386

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.0529

Gnomad4 SAS AF: 0.0667

Gnomad4 FIN AF: 0.0692

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.183

Alfa AF: 0.133 Hom.: 1121

Bravo AF: 0.174

Asia WGS AF: 0.0810 AC: 282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.2
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6577059; hg19: chr13-114300692;