6-4112813-A-T

Variant names:

• chr6-4112813-A-T
• rs853416
• ENST00000360378.6:n.488-2641A>T

Variant summary

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

The ENST00000427996.5(TEX56P):​n.664-9136A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 150,862 control chromosomes in the GnomAD database, including 6,998 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 0.30 (6998 hom., cov: 32)
• Consequence: TEX56P ENST00000427996.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.811
• 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000427996.5. 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.1050-2594A>T		intron	N/A
	TEX56P	NR_104464.3		n.672-9136A>T		intron	N/A
	TEX56P	NR_172627.1		n.1050-9136A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX56P	ENST00000360378.6	TSL:4	n.488-2641A>T		intron	N/A
	TEX56P	ENST00000427996.5	TSL:2	n.664-9136A>T		intron	N/A
	TEX56P	ENST00000436110.1	TSL:2	n.488-2594A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45643 AN: 150744 Hom.: 6994 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.331

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.303 AC: 45671 AN: 150862 Hom.: 6998 Cov.: 32 AF XY: 0.300 AC XY: 22066 AN XY: 73624

African (AFR) AF: 0.283 AC: 11626 AN: 41032

American (AMR) AF: 0.361 AC: 5478 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3460

East Asian (EAS) AF: 0.366 AC: 1873 AN: 5112

South Asian (SAS) AF: 0.248 AC: 1188 AN: 4792

European-Finnish (FIN) AF: 0.267 AC: 2749 AN: 10306

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20860 AN: 67702

Other (OTH) AF: 0.329 AC: 690 AN: 2096

Alfa AF: 0.289 Hom.: 776

Bravo AF: 0.310

Asia WGS AF: 0.293 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.7
DANN	Benign	0.65
PhyloP100		0.81
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

Other links and lift over

dbSNP: rs853416; hg19: chr6-4113047;