rs10146204

Positions:

• chr14-64352051-G-A

Variant summary

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

The ENST00000641216.1(ENSG00000284664):​n.234C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,984 control chromosomes in the GnomAD database, including 15,727 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 0.45 (15726 hom., cov: 31)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: ENST00000641216.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363

Genes affected

(HGNC:):

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000641216.1	n.234C>T		non_coding_transcript_exon_variant	1/2
TEX21P	ENST00000447107.1	n.981+2674C>T		intron_variant, non_coding_transcript_variant
	ENST00000641479.1	n.1218+1902C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67806 AN: 151856 Hom.: 15718 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.435

GnomAD4 exome AF: 0.500 AC: 5 AN: 10 Hom.: 1 Cov.: 0 AF XY: 0.375 AC XY: 3 AN XY: 8

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.446 AC: 67837 AN: 151974 Hom.: 15726 Cov.: 31 AF XY: 0.439 AC XY: 32591 AN XY: 74278

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.430

Alfa AF: 0.419 Hom.: 1715

Bravo AF: 0.451

Asia WGS AF: 0.363 AC: 1265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.7
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10146204; hg19: chr14-64818769;