chr13-20126789-A-G

Variant names:

• chr13-20126789-A-G
• rs747931
• ENST00000793259.1:n.125T>C

Variant summary

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

The ENST00000793259.1(ENSG00000303261):​n.125T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,000 control chromosomes in the GnomAD database, including 7,644 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 0.30 (7644 hom., cov: 30)
• Consequence: ENSG00000303261 ENST00000793259.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 7 publications found

Genes affected

ENSG00000303261 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793259.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303261	ENST00000793259.1		n.125T>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45128 AN: 151882 Hom.: 7649 Cov.: 30

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.297 AC: 45126 AN: 152000 Hom.: 7644 Cov.: 30 AF XY: 0.292 AC XY: 21676 AN XY: 74272

African (AFR) AF: 0.151 AC: 6263 AN: 41462

American (AMR) AF: 0.248 AC: 3793 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1717 AN: 3470

East Asian (EAS) AF: 0.104 AC: 540 AN: 5176

South Asian (SAS) AF: 0.319 AC: 1536 AN: 4812

European-Finnish (FIN) AF: 0.344 AC: 3633 AN: 10552

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26493 AN: 67938

Other (OTH) AF: 0.325 AC: 685 AN: 2108

Alfa AF: 0.363 Hom.: 13539

Bravo AF: 0.283

Asia WGS AF: 0.250 AC: 871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.43
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs747931; hg19: chr13-20700928;