NM_001385040.1:c.-43+41355C>T

Variant names:

• chr15-56285633-C-T
• rs2725854
• NM_001385040.1:c.-43+41355C>T

Variant summary

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

The NM_001385040.1(TEX9):​c.-43+41355C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,950 control chromosomes in the GnomAD database, including 10,524 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 0.35 (10524 hom., cov: 32)
• Consequence: TEX9 NM_001385040.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174
• Publications: 6 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001385040.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX9	NM_001385040.1		c.-43+41355C>T		intron	N/A	NP_001371969.1
	TEX9	NM_001385041.1		c.-168+41355C>T		intron	N/A	NP_001371970.1
	TEX9	NM_001385042.1		c.-107+41355C>T		intron	N/A	NP_001371971.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX9	ENST00000560827.6	TSL:3	c.-107+41355C>T		intron	N/A	ENSP00000452791.2

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52753 AN: 151832 Hom.: 10528 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.347 AC: 52756 AN: 151950 Hom.: 10524 Cov.: 32 AF XY: 0.347 AC XY: 25786 AN XY: 74242

African (AFR) AF: 0.147 AC: 6078 AN: 41452

American (AMR) AF: 0.384 AC: 5852 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1265 AN: 3466

East Asian (EAS) AF: 0.345 AC: 1780 AN: 5158

South Asian (SAS) AF: 0.307 AC: 1481 AN: 4824

European-Finnish (FIN) AF: 0.444 AC: 4680 AN: 10540

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30342 AN: 67956

Other (OTH) AF: 0.338 AC: 712 AN: 2106

Alfa AF: 0.408 Hom.: 6706

Bravo AF: 0.334

Asia WGS AF: 0.326 AC: 1132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.2
DANN	Benign	0.56
PhyloP100		0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2725854; hg19: chr15-56577831;