rs1887784

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-114658931-A-G
• chr9-114658931-A-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415101.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX53	ENST00000415101.1	TSL:3	n.101-2324T>C		intron	N/A
	ENSG00000294099	ENST00000720956.1		n.82-60A>G		intron	N/A
	ENSG00000294099	ENST00000720957.1		n.299-60A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1887784;

hg19: chr9-117421211;