chr13-30893774-T-C

Variant names:

• chr13-30893774-T-C
• rs117395
• ENST00000585870.6:n.1438-9714A>G

Variant summary

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

The ENST00000585870.6(TEX26-AS1):​n.1438-9714A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,180 control chromosomes in the GnomAD database, including 1,745 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 0.14 (1745 hom., cov: 32)
• Consequence: TEX26-AS1 ENST00000585870.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 4 publications found

Genes affected

TEX26-AS1 (HGNC:42784): (TEX26 antisense RNA 1)

LINC00398 (HGNC:42727): (long intergenic non-protein coding RNA 398)

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 (EAS) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX26-AS1	NR_038287.1	n.1438-9714A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX26-AS1	ENST00000585870.6	n.1438-9714A>G		intron_variant	Intron 2 of 3	2
TEX26-AS1	ENST00000588726.6	n.1438-10439A>G		intron_variant	Intron 2 of 2	5
TEX26-AS1	ENST00000592950.5	n.185+6140A>G		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21341 AN: 152062 Hom.: 1746 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0715

Gnomad ASJ AF: 0.0948

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.140 AC: 21340 AN: 152180 Hom.: 1745 Cov.: 32 AF XY: 0.140 AC XY: 10444 AN XY: 74414

African (AFR) AF: 0.190 AC: 7904 AN: 41494

American (AMR) AF: 0.0711 AC: 1088 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0948 AC: 329 AN: 3472

East Asian (EAS) AF: 0.349 AC: 1798 AN: 5158

South Asian (SAS) AF: 0.222 AC: 1072 AN: 4818

European-Finnish (FIN) AF: 0.0859 AC: 911 AN: 10602

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7870 AN: 68016

Other (OTH) AF: 0.119 AC: 252 AN: 2116

Alfa AF: 0.127 Hom.: 284

Bravo AF: 0.142

Asia WGS AF: 0.254 AC: 883 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	0.45
DANN	Benign	0.61
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs117395; hg19: chr13-31467911;