rs750696379

Variant names:

• chr6-4099018-C-A
• rs750696379
• ENST00000360378.6:n.307C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-4099018-C-A
• chr6-4099018-C-G
• chr6-4099018-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The ENST00000427996.5(TEX56P):​n.483C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: TEX56P ENST00000427996.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• Publications: 0 publications found

Genes affected

TEX56P (HGNC:):

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

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.36505124).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX56P	NR_104463.3	n.869C>A		non_coding_transcript_exon_variant	Exon 3 of 8
TEX56P	NR_104464.3	n.491C>A		non_coding_transcript_exon_variant	Exon 2 of 6
TEX56P	NR_172627.1	n.869C>A		non_coding_transcript_exon_variant	Exon 3 of 6
TEX56P	NR_172628.1	n.491C>A		non_coding_transcript_exon_variant	Exon 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX56P	ENST00000360378.6	n.307C>A		non_coding_transcript_exon_variant	Exon 2 of 3	4
TEX56P	ENST00000427996.5	n.483C>A		non_coding_transcript_exon_variant	Exon 2 of 6	2
TEX56P	ENST00000436110.1	n.307C>A		non_coding_transcript_exon_variant	Exon 2 of 7	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.51
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	18
DANN	Uncertain	0.99
DEOGEN2	Benign	0.027	T
Eigen	Benign	-0.020
Eigen_PC	Benign	-0.16
FATHMM_MKL	Benign	0.11	N
LIST_S2	Benign	0.78	T
M_CAP	Benign	0.011	T
MetaRNN	Benign	0.37	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.2	L
PhyloP100		1.9
PROVEAN	Pathogenic	-5.8	D
REVEL	Benign	0.12
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.52
MutPred		0.14		Loss of glycosylation at S35 (P = 0.1623);
MVP		0.28
MPC		0.39
ClinPred		0.99	D
GERP RS		4.0
Varity_R		0.56
gMVP		0.24

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs750696379; hg19: chr6-4099252;