rs767216

chrX-125324323-T-C

Variant summary

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

The NM_001195272.2(TEX13C):c.*643T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 111,073 control chromosomes in the GnomAD database, including 2,010 homozygotes. There are 5,954 hemizygotes in GnomAD. 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 0.19 (2010 hom., 5954 hem., cov: 23)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: TEX13C NM_001195272.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

Genes affected

TEX13C (HGNC:52277): (TEX13 family member C) Predicted to enable metal ion binding activity. [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=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX13C	NM_001195272.2	c.*643T>C		3_prime_UTR_variant	2/2	ENST00000695840.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX13C	ENST00000695840.1	c.*643T>C		3_prime_UTR_variant	2/2		NM_001195272.2	P1
TEX13C	ENST00000632600.2	c.*1222T>C		3_prime_UTR_variant	1/1			P1
TEX13C	ENST00000695841.1	c.*610T>C		3_prime_UTR_variant	2/2			P1

Frequencies

GnomAD3 genomes AF: 0.190 AC: 21115 AN: 111020 Hom.: 2006 Cov.: 23 AF XY: 0.178 AC XY: 5917 AN XY: 33274

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.0809

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.172

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 3 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 3

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.190 AC: 21159 AN: 111073 Hom.: 2010 Cov.: 23 AF XY: 0.179 AC XY: 5954 AN XY: 33337

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.171

Alfa AF: 0.157 Hom.: 1100

Bravo AF: 0.203

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	0.13
Dann	Benign	0.84

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: rs767216; hg19: chrX-124458172;