rs1887784

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001746908.3(LOC107987121):​n.299-60A>G variant causes a intron, non coding transcript 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: LOC107987121 XR_001746908.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167

Genes affected

LOC107987121 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107987121	XR_001746908.3	n.299-60A>G		intron_variant, non_coding_transcript_variant
LOC107987121	XR_007061744.1	n.154-60A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX53	ENST00000415101.1	n.101-2324T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.227

Alfa AF: 0.225 Hom.: 2219

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1887784; hg19: chr9-117421211;