rs2987981

Variant names:

• chr14-64368800-A-G
• rs2987981
• ENST00000447107.1:n.264+5603T>C

Variant summary

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

The ENST00000556556.2(TEX21P):​n.358+5596T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,044 control chromosomes in the GnomAD database, including 6,240 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 0.27 (6240 hom., cov: 32)
• Consequence: TEX21P ENST00000556556.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470

Genes affected

TEX21P (HGNC:35455): (testis expressed 21, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX21P	ENST00000447107.1	n.264+5603T>C		intron_variant	Intron 1 of 5	6
TEX21P	ENST00000556556.2	n.358+5596T>C		intron_variant	Intron 2 of 9	4
TEX21P	ENST00000641343.1	n.347+5596T>C		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40981 AN: 151926 Hom.: 6239 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.270 AC: 41002 AN: 152044 Hom.: 6240 Cov.: 32 AF XY: 0.264 AC XY: 19587 AN XY: 74306

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.263

Alfa AF: 0.249 Hom.: 6656

Bravo AF: 0.274

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2987981; hg19: chr14-64835518;