rs12023718

Positions:

• chr1-178522744-T-C

Variant summary

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

The NM_001170722.2(TEX35):​c.611-558T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 889,078 control chromosomes in the GnomAD database, including 7,611 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 (1818 hom., cov: 32)
  • Exomes 𝑓: 0.12 (5793 hom.)
• Consequence: TEX35 NM_001170722.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

Genes affected

TEX35 (HGNC:25366): (testis expressed 35) Located in microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX35	NM_001170722.2	c.611-558T>C		intron_variant			NP_001164193.1
TEX35	NM_001170724.2	c.587-558T>C		intron_variant			NP_001164195.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX35	ENST00000367639.1	c.611-558T>C		intron_variant		1		ENSP00000356611.1
TEX35	ENST00000419909.6	n.*341+1480T>C		intron_variant		2		ENSP00000430720.1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21625 AN: 152034 Hom.: 1802 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0628

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.143

GnomAD4 exome AF: 0.122 AC: 89742 AN: 736926 Hom.: 5793 AF XY: 0.122 AC XY: 42321 AN XY: 347932

Gnomad4 AFR exome AF: 0.239

Gnomad4 AMR exome AF: 0.0837

Gnomad4 ASJ exome AF: 0.134

Gnomad4 EAS exome AF: 0.0996

Gnomad4 SAS exome AF: 0.0923

Gnomad4 FIN exome AF: 0.0652

Gnomad4 NFE exome AF: 0.121

Gnomad4 OTH exome AF: 0.122

GnomAD4 genome AF: 0.142 AC: 21680 AN: 152152 Hom.: 1818 Cov.: 32 AF XY: 0.137 AC XY: 10209 AN XY: 74420

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0628

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.148

Alfa AF: 0.121 Hom.: 386

Bravo AF: 0.149

Asia WGS AF: 0.149 AC: 518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12023718; hg19: chr1-178491879;