ENST00000827138.1:n.300-1442T>A

Variant names:

• chr5-169472983-T-A
• rs13156607
• ENST00000827138.1:n.300-1442T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B.

Score: -2 - Likely Benign

-2

PM2BP4_Strong

The ENST00000827138.1(ENSG00000307563):​n.300-1442T>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: ENSG00000307563 ENST00000827138.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 11 publications found

Genes affected

ENSG00000307563 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377714	XR_941200.3	n.461-13047A>T		intron_variant	Intron 2 of 2
LOC105377715	XR_941204.3	n.241-1442T>A		intron_variant	Intron 2 of 3
LOC105377715	XR_941205.3	n.230+3743T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307563	ENST00000827138.1	n.300-1442T>A		intron_variant	Intron 2 of 4
ENSG00000307563	ENST00000827139.1	n.248+3743T>A		intron_variant	Intron 2 of 3
ENSG00000307563	ENST00000827140.1	n.264-1442T>A		intron_variant	Intron 2 of 4
ENSG00000307563	ENST00000827141.1	n.269-1442T>A		intron_variant	Intron 2 of 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	-0.90
CADD	Benign	0.34
DANN	Benign	0.43
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs13156607; hg19: chr5-168899987;