chr6-4108520-T-A

Variant names:

• chr6-4108520-T-A
• rs1815510
• ENST00000360378.6:n.488-6934T>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000427996.5(TEX56P):​n.663+9322T>A variant causes a intron 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 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX56P	NR_104463.3	n.1050-6887T>A		intron_variant	Intron 3 of 7
TEX56P	NR_104464.3	n.671+9322T>A		intron_variant	Intron 2 of 5
TEX56P	NR_172627.1	n.1049+9322T>A		intron_variant	Intron 3 of 5
TEX56P	NR_172628.1	n.671+9322T>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX56P	ENST00000360378.6	n.488-6934T>A		intron_variant	Intron 2 of 2	4
TEX56P	ENST00000427996.5	n.663+9322T>A		intron_variant	Intron 2 of 5	2
TEX56P	ENST00000436110.1	n.488-6887T>A		intron_variant	Intron 2 of 6	2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	13
DANN	Benign	0.87

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: rs1815510; hg19: chr6-4108754;