rs12023718

Variant names:

• chr1-178522744-T-C
• rs12023718
• ENST00000367639.1:c.611-558T>C

Variant summary

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

The ENST00000367639.1(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 ENST00000367639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 6 publications found

Genes affected

TEX35 (HGNC:25366): (testis expressed 35) Located in microtubule cytoskeleton. [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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000367639.1. 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
	TEX35	NM_001170722.2		c.611-558T>C		intron	N/A	NP_001164193.1
	TEX35	NM_001170724.2		c.587-558T>C		intron	N/A	NP_001164195.1
	TEX35	NM_032126.5	MANE Select	c.*304T>C		downstream_gene	N/A	NP_115502.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX35	ENST00000367639.1	TSL:1	c.611-558T>C		intron	N/A	ENSP00000356611.1
	TEX35	ENST00000419909.6	TSL:2	n.*341+1480T>C		intron	N/A	ENSP00000430720.1
	TEX35	ENST00000319416.7	TSL:1 MANE Select	c.*304T>C		downstream_gene	N/A	ENSP00000323795.2

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

African (AFR) AF: 0.239 AC: 3612 AN: 15090

American (AMR) AF: 0.0837 AC: 430 AN: 5136

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 929 AN: 6932

East Asian (EAS) AF: 0.0996 AC: 825 AN: 8284

South Asian (SAS) AF: 0.0923 AC: 1638 AN: 17742

European-Finnish (FIN) AF: 0.0652 AC: 245 AN: 3756

Middle Eastern (MID) AF: 0.135 AC: 225 AN: 1670

European-Non Finnish (NFE) AF: 0.121 AC: 78610 AN: 651916

Other (OTH) AF: 0.122 AC: 3228 AN: 26400

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

African (AFR) AF: 0.235 AC: 9743 AN: 41460

American (AMR) AF: 0.104 AC: 1587 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3472

East Asian (EAS) AF: 0.100 AC: 520 AN: 5184

South Asian (SAS) AF: 0.104 AC: 503 AN: 4826

European-Finnish (FIN) AF: 0.0628 AC: 667 AN: 10618

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7709 AN: 67998

Other (OTH) AF: 0.148 AC: 311 AN: 2106

Alfa AF: 0.123 Hom.: 495

Bravo AF: 0.149

Asia WGS AF: 0.149 AC: 518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.42
PhyloP100		0.31
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: rs12023718; hg19: chr1-178491879;