rs3813637

Positions:

• chr1-178522545-C-G
• chr1-178522545-C-T

Variant summary

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

The ENST00000319416.7(TEX35):​c.*105C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 1,328,354 control chromosomes in the GnomAD database, including 9,117 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 0.13 (1694 hom., cov: 33)
  • Exomes 𝑓: 0.11 (7423 hom.)
• Consequence: TEX35 ENST00000319416.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

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 = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX35	NM_032126.5	c.*105C>G		3_prime_UTR_variant	9/9	ENST00000319416.7	NP_115502.2
TEX35	NM_001170722.2	c.611-757C>G		intron_variant			NP_001164193.1
TEX35	NM_001170724.2	c.587-757C>G		intron_variant			NP_001164195.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX35	ENST00000319416.7	c.*105C>G		3_prime_UTR_variant	9/9	1	NM_032126.5	ENSP00000323795	A2

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20067 AN: 152070 Hom.: 1681 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0847

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.0513

Gnomad SAS AF: 0.0559

Gnomad FIN AF: 0.0611

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.121

GnomAD4 exome AF: 0.108 AC: 126854 AN: 1176166 Hom.: 7423 Cov.: 29 AF XY: 0.107 AC XY: 60199 AN XY: 563714

Gnomad4 AFR exome AF: 0.241

Gnomad4 AMR exome AF: 0.0653

Gnomad4 ASJ exome AF: 0.0934

Gnomad4 EAS exome AF: 0.0609

Gnomad4 SAS exome AF: 0.0543

Gnomad4 FIN exome AF: 0.0662

Gnomad4 NFE exome AF: 0.110

Gnomad4 OTH exome AF: 0.106

GnomAD4 genome AF: 0.132 AC: 20119 AN: 152188 Hom.: 1694 Cov.: 33 AF XY: 0.126 AC XY: 9380 AN XY: 74388

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.0843

Gnomad4 ASJ AF: 0.0922

Gnomad4 EAS AF: 0.0510

Gnomad4 SAS AF: 0.0553

Gnomad4 FIN AF: 0.0611

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0315 Hom.: 14

Bravo AF: 0.138

Asia WGS AF: 0.117 AC: 406 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	0.97
DANN	Benign	0.80

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

Publications

LitVar

Other links and lift over

dbSNP: rs3813637; hg19: chr1-178491680;