rs6563141

Positions:

• chr13-79862757-G-A
• chr13-79862757-G-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 0.252 in 152,100 control chromosomes in the GnomAD database, including 6,576 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 0.25 (6576 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 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: 0.252 AC: 38333 AN: 151982 Hom.: 6574 Cov.: 33

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.0801

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.252 AC: 38365 AN: 152100 Hom.: 6576 Cov.: 33 AF XY: 0.250 AC XY: 18565 AN XY: 74366

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.0801

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.235

Alfa AF: 0.162 Hom.: 1115

Bravo AF: 0.274

Asia WGS AF: 0.252 AC: 874 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.32
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: rs6563141; hg19: chr13-80436892;