rs6563141

Variant names:

• chr13-79862757-G-A
• rs6563141
• ENST00000780129.1:n.251+2346C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-79862757-G-A
• chr13-79862757-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000780129.1(ENSG00000301598):​n.251+2346C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000301598 ENST00000780129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• Publications: 2 publications found

Genes affected

ENSG00000301598 (HGNC:):

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301598	ENST00000780129.1	n.251+2346C>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.487 AC: 20183 AN: 41466

American (AMR) AF: 0.244 AC: 3720 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3466

East Asian (EAS) AF: 0.283 AC: 1464 AN: 5168

South Asian (SAS) AF: 0.190 AC: 914 AN: 4818

European-Finnish (FIN) AF: 0.0801 AC: 849 AN: 10602

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10053 AN: 67998

Other (OTH) AF: 0.235 AC: 497 AN: 2112

Alfa AF: 0.166 Hom.: 1327

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
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs6563141; hg19: chr13-80436892;