NM_001395496.1:c.828+327C>T

Variant names:

• chr15-56395161-C-T
• rs6493856
• NM_001395496.1:c.828+327C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001395496.1(TEX9):​c.828+327C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TEX9 NM_001395496.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 3 publications found

Genes affected

TEX9 (HGNC:29585): (testis expressed 9)

ENSG00000259941 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395496.1. 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
	TEX9	NM_001395496.1	MANE Select	c.828+327C>T		intron	N/A	NP_001382425.1
	TEX9	NM_198524.3		c.828+327C>T		intron	N/A	NP_940926.1
	TEX9	NM_001385046.1		c.696+327C>T		intron	N/A	NP_001371975.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX9	ENST00000696102.1	MANE Select	c.828+327C>T		intron	N/A	ENSP00000512397.1
	TEX9	ENST00000352903.6	TSL:1	c.828+327C>T		intron	N/A	ENSP00000342169.2
	TEX9	ENST00000558083.2	TSL:2	n.*1028C>T		non_coding_transcript_exon	Exon 8 of 8	ENSP00000453398.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 150948 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 75684

African (AFR) AF: 0.00 AC: 0 AN: 5164

American (AMR) AF: 0.00 AC: 0 AN: 4850

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6348

East Asian (EAS) AF: 0.00 AC: 0 AN: 13702

South Asian (SAS) AF: 0.00 AC: 0 AN: 1922

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8708

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 828

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 98780

Other (OTH) AF: 0.00 AC: 0 AN: 10646

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1267

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.76
PhyloP100		0.14
PromoterAI		-0.0062	Neutral

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: rs6493856; hg19: chr15-56687359;