chr10-125576346-G-A

Variant names:

• chr10-125576346-G-A
• rs2304264
• ENST00000446081.5:n.508G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

TEX36-AS1 (HGNC:49500): (TEX36 antisense RNA 1)

TEX36 (HGNC:31653): (testis expressed 36)

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446081.5. 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
	TEX36-AS1	NR_023362.1		n.508G>A		non_coding_transcript_exon	Exon 4 of 5
	TEX36	NM_001318133.2		c.*403C>T		downstream_gene	N/A	NP_001305062.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX36-AS1	ENST00000446081.5	TSL:1	n.508G>A		non_coding_transcript_exon	Exon 4 of 5
	TEX36-AS1	ENST00000816071.1		n.396G>A		non_coding_transcript_exon	Exon 3 of 4
	TEX36-AS1	ENST00000816072.1		n.266G>A		non_coding_transcript_exon	Exon 2 of 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

African (AFR) AF: 0.00873 AC: 11 AN: 1260

American (AMR) AF: 0.151 AC: 452 AN: 2992

Ashkenazi Jewish (ASJ) AF: 0.0298 AC: 18 AN: 604

East Asian (EAS) AF: 0.153 AC: 294 AN: 1926

South Asian (SAS) AF: 0.0218 AC: 49 AN: 2248

European-Finnish (FIN) AF: 0.0720 AC: 38 AN: 528

Middle Eastern (MID) AF: 0.0135 AC: 1 AN: 74

European-Non Finnish (NFE) AF: 0.0773 AC: 1087 AN: 14064

Other (OTH) AF: 0.0707 AC: 83 AN: 1174

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

African (AFR) AF: 0.0171 AC: 709 AN: 41566

American (AMR) AF: 0.126 AC: 1925 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0421 AC: 146 AN: 3472

East Asian (EAS) AF: 0.168 AC: 872 AN: 5178

South Asian (SAS) AF: 0.0309 AC: 149 AN: 4826

European-Finnish (FIN) AF: 0.0865 AC: 918 AN: 10618

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0804 AC: 5473 AN: 68030

Other (OTH) AF: 0.0776 AC: 164 AN: 2114

Alfa AF: 0.0728 Hom.: 1091

Bravo AF: 0.0719

Asia WGS AF: 0.0850 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.74
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2304264; hg19: chr10-127264915;