dbSNP rs7067478: ENSG00000290323:n.219-2288T>G (chrY-7779316-A-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000442584.2(ENSG00000290323):n.219-2288T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: 0)

Consequence

ENSG00000290323
ENST00000442584.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.498

Variant links:

Genes affected

ENSG00000290323 (HGNC:18840): (testis expressed transcript, Y-linked 16)

ENSG00000290323 links:

LOC107987339 (HGNC:):

LOC107987339 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987339	XR_001756056.2 link	n.*151T>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000290323	ENST00000442584.2 link	n.219-2288T>G	intron_variant	Intron 2 of 4	5
ENSG00000290323	ENST00000651261.1 link	n.115-2612T>G	intron_variant	Intron 1 of 7
ENSG00000290323	ENST00000652723.1 link	n.1027-2612T>G	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.93

DANN

Benign

0.32

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over