10-125576346-G-A

Position:

• chr10-125576346-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000446081.5(TEX36-AS1):​n.508G>A 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 0.0702 in 177,178 control chromosomes in the GnomAD database, including 649 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 0.068 (530 hom., cov: 33)
  • Exomes 𝑓: 0.082 (119 hom.)
• Consequence: TEX36-AS1 ENST00000446081.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

Genes affected

TEX36-AS1 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX36-AS1	NR_023362.1	n.508G>A		non_coding_transcript_exon_variant	4/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX36-AS1	ENST00000446081.5	n.508G>A		non_coding_transcript_exon_variant	4/5	1
TEX36-AS1	ENST00000431861.1	n.227+345G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0683 AC: 10396 AN: 152190 Hom.: 527 Cov.: 33

Gnomad AFR AF: 0.0171

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0306

Gnomad FIN AF: 0.0865

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0804

Gnomad OTH AF: 0.0774

GnomAD4 exome AF: 0.0817 AC: 2033 AN: 24870 Hom.: 119 Cov.: 0 AF XY: 0.0819 AC XY: 1049 AN XY: 12804

Gnomad4 AFR exome AF: 0.00873

Gnomad4 AMR exome AF: 0.151

Gnomad4 ASJ exome AF: 0.0298

Gnomad4 EAS exome AF: 0.153

Gnomad4 SAS exome AF: 0.0218

Gnomad4 FIN exome AF: 0.0720

Gnomad4 NFE exome AF: 0.0773

Gnomad4 OTH exome AF: 0.0707

GnomAD4 genome AF: 0.0683 AC: 10402 AN: 152308 Hom.: 530 Cov.: 33 AF XY: 0.0695 AC XY: 5180 AN XY: 74486

Gnomad4 AFR AF: 0.0171

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.0309

Gnomad4 FIN AF: 0.0865

Gnomad4 NFE AF: 0.0804

Gnomad4 OTH AF: 0.0776

Alfa AF: 0.0746 Hom.: 763

Bravo AF: 0.0719

Asia WGS AF: 0.0850 AC: 294 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	4.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2304264; hg19: chr10-127264915;