rs10146204

Variant names:

• chr14-64352051-G-A
• rs10146204
• ENST00000641216.1:n.234C>T

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000284664 ENST00000641216.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363
• Publications: 9 publications found

Genes affected

ENSG00000284664 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284664	ENST00000641216.1	n.234C>T		non_coding_transcript_exon_variant	Exon 1 of 2
TEX21P	ENST00000447107.1	n.981+2674C>T		intron_variant	Intron 4 of 5	6
ENSG00000293482	ENST00000556556.2	n.1191+1950C>T		intron_variant	Intron 7 of 9	4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 5 AN: 10

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.569 AC: 23599 AN: 41456

American (AMR) AF: 0.378 AC: 5761 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1750 AN: 3466

East Asian (EAS) AF: 0.273 AC: 1409 AN: 5162

South Asian (SAS) AF: 0.427 AC: 2059 AN: 4820

European-Finnish (FIN) AF: 0.326 AC: 3444 AN: 10550

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28275 AN: 67950

Other (OTH) AF: 0.430 AC: 907 AN: 2110

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
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10146204; hg19: chr14-64818769;