rs3813637

Variant names:

• chr1-178522545-C-G
• rs3813637
• NM_032126.5:c.*105C>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_032126.5(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 NM_032126.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 3 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 = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX35	NM_032126.5	c.*105C>G		3_prime_UTR_variant	Exon 9 of 9	ENST00000319416.7	NP_115502.2
TEX35	NM_001170722.2	c.611-757C>G		intron_variant	Intron 8 of 8		NP_001164193.1
TEX35	NM_001170724.2	c.587-757C>G		intron_variant	Intron 8 of 8		NP_001164195.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX35	ENST00000319416.7	c.*105C>G		3_prime_UTR_variant	Exon 9 of 9	1	NM_032126.5	ENSP00000323795.2

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

African (AFR) AF: 0.241 AC: 6294 AN: 26162

American (AMR) AF: 0.0653 AC: 1161 AN: 17782

Ashkenazi Jewish (ASJ) AF: 0.0934 AC: 1600 AN: 17128

East Asian (EAS) AF: 0.0609 AC: 1860 AN: 30556

South Asian (SAS) AF: 0.0543 AC: 2033 AN: 37448

European-Finnish (FIN) AF: 0.0662 AC: 2167 AN: 32758

Middle Eastern (MID) AF: 0.147 AC: 708 AN: 4826

European-Non Finnish (NFE) AF: 0.110 AC: 105956 AN: 961618

Other (OTH) AF: 0.106 AC: 5075 AN: 47888

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

African (AFR) AF: 0.238 AC: 9895 AN: 41510

American (AMR) AF: 0.0843 AC: 1289 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0922 AC: 320 AN: 3472

East Asian (EAS) AF: 0.0510 AC: 264 AN: 5178

South Asian (SAS) AF: 0.0553 AC: 267 AN: 4826

European-Finnish (FIN) AF: 0.0611 AC: 647 AN: 10594

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7074 AN: 68004

Other (OTH) AF: 0.125 AC: 265 AN: 2114

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
PhyloP100		-0.24
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: rs3813637; hg19: chr1-178491680;