rs6477523

Variant names:

• chr9-106502795-G-A
• rs6477523
• ENST00000425709.3:n.170+51907G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-106502795-G-A
• chr9-106502795-G-C
• chr9-106502795-G-T

Variant summary

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

The ENST00000425709.3(LINC01505):​n.170+51907G>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: LINC01505 ENST00000425709.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 2 publications found

Genes affected

LINC01505 (HGNC:51186): (long intergenic non-protein coding RNA 1505)

LOC107987108 (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=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987108	XR_001746870.2	n.2033-55677G>A		intron_variant	Intron 3 of 5
LOC107987108	XR_007061711.1	n.222+2290G>A		intron_variant	Intron 2 of 4
LOC107987108	XR_007061712.1	n.73+51907G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01505	ENST00000425709.3	n.170+51907G>A		intron_variant	Intron 1 of 3	1
LINC01505	ENST00000411451.3	n.74+51907G>A		intron_variant	Intron 1 of 5	3
LINC01505	ENST00000435485.5	n.446+2290G>A		intron_variant	Intron 4 of 6	5

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	-0.92
CADD	Benign	0.20
DANN	Benign	0.66
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6477523; hg19: chr9-109265076;