rs6577059

Variant names:

• chr13-113646377-C-T
• rs6577059

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 0.163 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
• Publications: 5 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.294 AC: 12203 AN: 41452

American (AMR) AF: 0.131 AC: 1998 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3466

East Asian (EAS) AF: 0.0529 AC: 274 AN: 5180

South Asian (SAS) AF: 0.0667 AC: 321 AN: 4816

European-Finnish (FIN) AF: 0.0692 AC: 734 AN: 10604

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8044 AN: 67980

Other (OTH) AF: 0.183 AC: 387 AN: 2112

Alfa AF: 0.135 Hom.: 1670

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
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs6577059; hg19: chr13-114300692;