chr15-56254014-C-T

Variant names:

• chr15-56254014-C-T
• rs2713935
• NM_001385040.1:c.-43+9736C>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+9736C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,840 control chromosomes in the GnomAD database, including 17,121 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 0.47 (17121 hom., cov: 31)
• Consequence: TEX9 NM_001385040.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416
• Publications: 7 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX9	NM_001385040.1	c.-43+9736C>T		intron_variant	Intron 1 of 9		NP_001371969.1
TEX9	NM_001385041.1	c.-168+9736C>T		intron_variant	Intron 1 of 11		NP_001371970.1
TEX9	NM_001385042.1	c.-107+9736C>T		intron_variant	Intron 1 of 10		NP_001371971.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX9	ENST00000560827.6	c.-107+9736C>T		intron_variant	Intron 1 of 10	3		ENSP00000452791.2

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71481 AN: 151722 Hom.: 17113 Cov.: 31

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.471 AC: 71537 AN: 151840 Hom.: 17121 Cov.: 31 AF XY: 0.469 AC XY: 34843 AN XY: 74224

African (AFR) AF: 0.409 AC: 16911 AN: 41392

American (AMR) AF: 0.502 AC: 7653 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1392 AN: 3468

East Asian (EAS) AF: 0.454 AC: 2344 AN: 5162

South Asian (SAS) AF: 0.375 AC: 1802 AN: 4802

European-Finnish (FIN) AF: 0.531 AC: 5596 AN: 10538

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.504 AC: 34249 AN: 67932

Other (OTH) AF: 0.452 AC: 949 AN: 2100

Alfa AF: 0.485 Hom.: 21769

Bravo AF: 0.467

Asia WGS AF: 0.472 AC: 1640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.85
DANN	Benign	0.44
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs2713935; hg19: chr15-56546212;