ENST00000483580.5:n.552C>T

Variant names:

• chr6-4101333-C-T
• rs626080
• ENST00000483580.5:n.552C>T

Variant summary

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

The ENST00000483580.5(TEX56P):​n.552C>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 0.463 in 977,188 control chromosomes in the GnomAD database, including 106,004 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 0.47 (16863 hom., cov: 32)
  • Exomes 𝑓: 0.46 (89141 hom.)
• Consequence: TEX56P ENST00000483580.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 6 publications found

Genes affected

TEX56P (HGNC:):

TEX56P (HGNC:21620): (testis expressed 56, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000483580.5. 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
	TEX56P	NR_104463.3		n.1049+2135C>T		intron	N/A
	TEX56P	NR_104464.3		n.671+2135C>T		intron	N/A
	TEX56P	NR_172627.1		n.1049+2135C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX56P	ENST00000483580.5	TSL:4	n.552C>T		non_coding_transcript_exon	Exon 3 of 3
	TEX56P	ENST00000360378.6	TSL:4	n.487+2135C>T		intron	N/A
	TEX56P	ENST00000427996.5	TSL:2	n.663+2135C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70812 AN: 151774 Hom.: 16839 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.477

GnomAD4 exome AF: 0.463 AC: 381721 AN: 825296 Hom.: 89141 Cov.: 21 AF XY: 0.462 AC XY: 176150 AN XY: 381274

African (AFR) AF: 0.527 AC: 8241 AN: 15640

American (AMR) AF: 0.425 AC: 412 AN: 970

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1887 AN: 5086

East Asian (EAS) AF: 0.373 AC: 1334 AN: 3578

South Asian (SAS) AF: 0.332 AC: 5407 AN: 16302

European-Finnish (FIN) AF: 0.530 AC: 142 AN: 268

Middle Eastern (MID) AF: 0.396 AC: 634 AN: 1602

European-Non Finnish (NFE) AF: 0.466 AC: 351622 AN: 754802

Other (OTH) AF: 0.445 AC: 12042 AN: 27048

GnomAD4 genome AF: 0.467 AC: 70895 AN: 151892 Hom.: 16863 Cov.: 32 AF XY: 0.467 AC XY: 34690 AN XY: 74218

African (AFR) AF: 0.518 AC: 21445 AN: 41408

American (AMR) AF: 0.448 AC: 6824 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1254 AN: 3470

East Asian (EAS) AF: 0.371 AC: 1915 AN: 5164

South Asian (SAS) AF: 0.329 AC: 1587 AN: 4822

European-Finnish (FIN) AF: 0.553 AC: 5822 AN: 10520

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30601 AN: 67956

Other (OTH) AF: 0.475 AC: 1000 AN: 2106

Alfa AF: 0.443 Hom.: 25086

Bravo AF: 0.464

Asia WGS AF: 0.349 AC: 1214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.24
DANN	Benign	0.70
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs626080;

hg19: chr6-4101567;