chr9-114658931-A-G

Variant names:

• chr9-114658931-A-G
• rs1887784
• ENST00000415101.1:n.101-2324T>C

Variant summary

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

The ENST00000415101.1(TEX53):​n.101-2324T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,172 control chromosomes in the GnomAD database, including 3,457 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 0.21 (3457 hom., cov: 32)
• Consequence: TEX53 ENST00000415101.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 3 publications found

Genes affected

TEX53 (HGNC:53655): (testis expressed 53)

ENSG00000294099 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987121	XR_001746908.3	n.299-60A>G		intron_variant	Intron 1 of 1
LOC107987121	XR_007061744.1	n.154-60A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX53	ENST00000415101.1	n.101-2324T>C		intron_variant	Intron 1 of 1	3
ENSG00000294099	ENST00000720956.1	n.82-60A>G		intron_variant	Intron 1 of 1
ENSG00000294099	ENST00000720957.1	n.299-60A>G		intron_variant	Intron 1 of 1
ENSG00000294099	ENST00000720958.1	n.409-60A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31735 AN: 152054 Hom.: 3441 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.209 AC: 31775 AN: 152172 Hom.: 3457 Cov.: 32 AF XY: 0.211 AC XY: 15667 AN XY: 74398

African (AFR) AF: 0.163 AC: 6771 AN: 41538

American (AMR) AF: 0.249 AC: 3813 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1114 AN: 3466

East Asian (EAS) AF: 0.158 AC: 820 AN: 5176

South Asian (SAS) AF: 0.287 AC: 1381 AN: 4808

European-Finnish (FIN) AF: 0.184 AC: 1949 AN: 10588

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15058 AN: 67990

Other (OTH) AF: 0.227 AC: 480 AN: 2116

Alfa AF: 0.223 Hom.: 2939

Bravo AF: 0.211

Asia WGS AF: 0.244 AC: 849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.75
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1887784; hg19: chr9-117421211;