rs8057477

Variant names:

• chr16-76716223-T-A
• rs8057477
• ENST00000563764.2:n.*122+80600T>A

Your query was ambiguous. Multiple possible variants found:

• chr16-76716223-T-A
• chr16-76716223-T-C
• chr16-76716223-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000563764.2(ENSG00000287694):​n.*122+80600T>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: 31)
• Consequence: ENSG00000287694 ENST00000563764.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 3 publications found

Genes affected

ENSG00000287694 (HGNC:):

LINC02125 (HGNC:52982): (long intergenic non-protein coding RNA 2125)

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287694	ENST00000563764.2	n.*122+80600T>A		intron_variant	Intron 3 of 3	3		ENSP00000455258.1
LINC02125	ENST00000567777.2	n.245-20094T>A		intron_variant	Intron 2 of 4	3
LINC02125	ENST00000751836.1	n.339-20094T>A		intron_variant	Intron 2 of 4
LINC02125	ENST00000751837.1	n.163-20094T>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.40
PhyloP100		-0.63

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: rs8057477; hg19: chr16-76750120;