rs2987981

Positions:

• chr14-64368800-A-G

Variant summary

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

The ENST00000447107.1(TEX21P):​n.264+5603T>C 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 0.27 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 ENST00000447107.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470

Genes affected

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

(HGNC:):

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX21P	ENST00000447107.1	n.264+5603T>C		intron_variant, non_coding_transcript_variant
	ENST00000641479.1	n.571-11297T>C		intron_variant, non_coding_transcript_variant

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;