rs1854953

Variant names:

• chr13-30944458-G-A
• rs1854953
• NM_152325.3:c.146+4680G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-30944458-G-A
• chr13-30944458-G-T

Variant summary

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

The NM_152325.3(TEX26):​c.146+4680G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 150,906 control chromosomes in the GnomAD database, including 4,655 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 0.25 (4655 hom., cov: 32)
• Consequence: TEX26 NM_152325.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356
• Publications: 2 publications found

Genes affected

TEX26 (HGNC:28622): (testis expressed 26) Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152325.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX26	NM_152325.3	MANE Select	c.146+4680G>A		intron	N/A	NP_689538.1	Q8N6G2
	TEX26	NM_001353388.2		c.-525-8202G>A		intron	N/A	NP_001340317.1
	TEX26	NM_001353389.2		c.-247-8202G>A		intron	N/A	NP_001340318.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX26	ENST00000380473.8	TSL:1 MANE Select	c.146+4680G>A		intron	N/A	ENSP00000369840.3	Q8N6G2
	TEX26	ENST00000944411.1		c.61+11682G>A		intron	N/A	ENSP00000614470.1
	TEX26	ENST00000944412.1		c.61+11682G>A		intron	N/A	ENSP00000614471.1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37030 AN: 150788 Hom.: 4647 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.246 AC: 37062 AN: 150906 Hom.: 4655 Cov.: 32 AF XY: 0.247 AC XY: 18199 AN XY: 73692

African (AFR) AF: 0.258 AC: 10638 AN: 41234

American (AMR) AF: 0.207 AC: 3131 AN: 15130

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 995 AN: 3462

East Asian (EAS) AF: 0.439 AC: 2257 AN: 5144

South Asian (SAS) AF: 0.321 AC: 1537 AN: 4788

European-Finnish (FIN) AF: 0.203 AC: 2104 AN: 10366

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15598 AN: 67482

Other (OTH) AF: 0.258 AC: 541 AN: 2096

Alfa AF: 0.119 Hom.: 205

Bravo AF: 0.246

Asia WGS AF: 0.353 AC: 1221 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.57
PhyloP100		0.36
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1854953; hg19: chr13-31518595;