chr13-27356094-C-T

Variant names:

• chr13-27356094-C-T
• rs9512645
• ENST00000793090.1:n.107+2601C>T

Variant summary

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

The ENST00000793090.1(ENSG00000303231):​n.107+2601C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,256 control chromosomes in the GnomAD database, including 2,306 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 0.15 (2306 hom., cov: 32)
• Consequence: ENSG00000303231 ENST00000793090.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818
• Publications: 3 publications found

Genes affected

ENSG00000303231 (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 (SAS) allele frequency at 95% confidence interval = 0.355 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
ENSG00000303231	ENST00000793090.1	n.107+2601C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22898 AN: 152138 Hom.: 2308 Cov.: 32

Gnomad AFR AF: 0.0386

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0371

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.150 AC: 22897 AN: 152256 Hom.: 2306 Cov.: 32 AF XY: 0.147 AC XY: 10908 AN XY: 74438

African (AFR) AF: 0.0385 AC: 1600 AN: 41566

American (AMR) AF: 0.129 AC: 1973 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3472

East Asian (EAS) AF: 0.0372 AC: 193 AN: 5184

South Asian (SAS) AF: 0.369 AC: 1780 AN: 4818

European-Finnish (FIN) AF: 0.108 AC: 1142 AN: 10602

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14975 AN: 68008

Other (OTH) AF: 0.162 AC: 342 AN: 2116

Alfa AF: 0.168 Hom.: 422

Bravo AF: 0.141

Asia WGS AF: 0.200 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.68
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs9512645; hg19: chr13-27930231;