17-58567455-T-C

Variant names:

• chr17-58567455-T-C
• rs12944693
• NM_031272.5:c.3887-1631A>G

Variant summary

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

The NM_031272.5(TEX14):​c.3887-1631A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0419 in 152,174 control chromosomes in the GnomAD database, including 199 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 0.042 (199 hom., cov: 32)
• Consequence: TEX14 NM_031272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.594
• Publications: 6 publications found

Genes affected

TEX14 (HGNC:11737): (testis expressed 14, intercellular bridge forming factor) The protein encoded by this gene is necessary for intercellular bridges in germ cells, which are required for spermatogenesis. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2011]

SEPTIN4-AS1 (HGNC:51345): (SEPTIN4 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0609 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031272.5. 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
	TEX14	NM_031272.5	MANE Select	c.3887-1631A>G		intron	N/A	NP_112562.3
	TEX14	NM_001201457.2		c.4025-1631A>G		intron	N/A	NP_001188386.1
	TEX14	NM_198393.4		c.4007-1631A>G		intron	N/A	NP_938207.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX14	ENST00000349033.10	TSL:5 MANE Select	c.3887-1631A>G		intron	N/A	ENSP00000268910.8
	TEX14	ENST00000240361.12	TSL:1	c.4025-1631A>G		intron	N/A	ENSP00000240361.8
	TEX14	ENST00000389934.7	TSL:1	c.4007-1631A>G		intron	N/A	ENSP00000374584.3

Frequencies

GnomAD3 genomes AF: 0.0419 AC: 6373 AN: 152056 Hom.: 198 Cov.: 32

Gnomad AFR AF: 0.0109

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0239

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0523

Gnomad FIN AF: 0.0641

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0624

Gnomad OTH AF: 0.0349

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0419 AC: 6372 AN: 152174 Hom.: 199 Cov.: 32 AF XY: 0.0415 AC XY: 3085 AN XY: 74398

African (AFR) AF: 0.0108 AC: 450 AN: 41536

American (AMR) AF: 0.0239 AC: 365 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0501 AC: 174 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5172

South Asian (SAS) AF: 0.0525 AC: 253 AN: 4816

European-Finnish (FIN) AF: 0.0641 AC: 679 AN: 10588

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0625 AC: 4247 AN: 68000

Other (OTH) AF: 0.0336 AC: 71 AN: 2116

Alfa AF: 0.0532 Hom.: 440

Bravo AF: 0.0360

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.45
PhyloP100		0.59
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: rs12944693; hg19: chr17-56644816;