6-4101333-C-T

Variant summary

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

The NR_104463.3(TEX56P):n.1049+2135C>T 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 0.463 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 NR_104463.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEX56P	NR_104463.3	n.1049+2135C>T		intron_variant, non_coding_transcript_variant
TEX56P	NR_104464.3	n.671+2135C>T		intron_variant, non_coding_transcript_variant
TEX56P	NR_172627.1	n.1049+2135C>T		intron_variant, non_coding_transcript_variant
TEX56P	NR_172628.1	n.671+2135C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEX56P	ENST00000642280.1	n.392+2135C>T		intron_variant, non_coding_transcript_variant
TEX56P	ENST00000643110.1	n.1049+2135C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 0.527

Gnomad4 AMR exome AF: 0.425

Gnomad4 ASJ exome AF: 0.371

Gnomad4 EAS exome AF: 0.373

Gnomad4 SAS exome AF: 0.332

Gnomad4 FIN exome AF: 0.530

Gnomad4 NFE exome AF: 0.466

Gnomad4 OTH exome AF: 0.445

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

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.475

Alfa AF: 0.439 Hom.: 19299

Bravo AF: 0.464

Asia WGS AF: 0.349 AC: 1214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.24
Dann	Benign	0.70

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

Publications

LitVar

Other links and lift over

dbSNP: rs626080; hg19: chr6-4101567;