14-64347593-C-T

Variant names:

• chr14-64347593-C-T
• rs1256112
• ENST00000447107.1:n.1149G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000556556.2(ENSG00000293482):​n.1247G>A 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 0.61 in 409,208 control chromosomes in the GnomAD database, including 79,420 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 0.67 (36020 hom., cov: 32)
  • Exomes 𝑓: 0.58 (43400 hom.)
• Consequence: ENSG00000293482 ENST00000556556.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.96
• Publications: 16 publications found

Genes affected

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

ENSG00000293482 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556556.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX21P	NR_033777.1		n.19G>A		non_coding_transcript_exon	Exon 1 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX21P	ENST00000447107.1	TSL:6	n.1149G>A		non_coding_transcript_exon	Exon 5 of 6
	ENSG00000293482	ENST00000556556.2	TSL:4	n.1247G>A		non_coding_transcript_exon	Exon 8 of 10
	ENSG00000293482	ENST00000641343.1		n.1071G>A		non_coding_transcript_exon	Exon 6 of 8

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101751 AN: 152002 Hom.: 35967 Cov.: 32

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.651

GnomAD2 exomes AF: 0.595 AC: 63842 AN: 107380 AF XY: 0.587

Gnomad AFR exome AF: 0.922

Gnomad AMR exome AF: 0.555

Gnomad ASJ exome AF: 0.644

Gnomad EAS exome AF: 0.720

Gnomad FIN exome AF: 0.521

Gnomad NFE exome AF: 0.572

Gnomad OTH exome AF: 0.589

GnomAD4 exome AF: 0.575 AC: 147952 AN: 257086 Hom.: 43400 Cov.: 0 AF XY: 0.569 AC XY: 84624 AN XY: 148768

African (AFR) AF: 0.915 AC: 6352 AN: 6944

American (AMR) AF: 0.556 AC: 11060 AN: 19888

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 5969 AN: 9294

East Asian (EAS) AF: 0.715 AC: 6125 AN: 8570

South Asian (SAS) AF: 0.522 AC: 25994 AN: 49778

European-Finnish (FIN) AF: 0.525 AC: 5588 AN: 10642

Middle Eastern (MID) AF: 0.612 AC: 1567 AN: 2562

European-Non Finnish (NFE) AF: 0.569 AC: 78160 AN: 137392

Other (OTH) AF: 0.594 AC: 7137 AN: 12016

GnomAD4 genome AF: 0.670 AC: 101862 AN: 152122 Hom.: 36020 Cov.: 32 AF XY: 0.663 AC XY: 49325 AN XY: 74352

African (AFR) AF: 0.913 AC: 37939 AN: 41534

American (AMR) AF: 0.578 AC: 8835 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2263 AN: 3470

East Asian (EAS) AF: 0.721 AC: 3725 AN: 5170

South Asian (SAS) AF: 0.533 AC: 2572 AN: 4824

European-Finnish (FIN) AF: 0.533 AC: 5618 AN: 10538

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38656 AN: 67984

Other (OTH) AF: 0.648 AC: 1369 AN: 2114

Alfa AF: 0.612 Hom.: 58752

Bravo AF: 0.685

Asia WGS AF: 0.648 AC: 2252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	17
DANN	Benign	0.72
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs1256112; hg19: chr14-64814311;