ENST00000425709.3:n.170+51907G>T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000425709.3(LINC01505):​n.170+51907G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,016 control chromosomes in the GnomAD database, including 21,079 homozygotes. 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: 𝑓 0.52 (21079 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987108	XR_001746870.2	n.2033-55677G>T		intron_variant	Intron 3 of 5
LOC107987108	XR_007061711.1	n.222+2290G>T		intron_variant	Intron 2 of 4
LOC107987108	XR_007061712.1	n.73+51907G>T		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>T		intron_variant	Intron 1 of 3	1
LINC01505	ENST00000411451.3	n.74+51907G>T		intron_variant	Intron 1 of 5	3
LINC01505	ENST00000435485.5	n.446+2290G>T		intron_variant	Intron 4 of 6	5

Frequencies

GnomAD3 genomes AF: 0.520 AC: 79034 AN: 151898 Hom.: 21028 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.521 AC: 79149 AN: 152016 Hom.: 21079 Cov.: 32 AF XY: 0.518 AC XY: 38459 AN XY: 74278

African (AFR) AF: 0.623 AC: 25814 AN: 41466

American (AMR) AF: 0.546 AC: 8344 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1316 AN: 3468

East Asian (EAS) AF: 0.382 AC: 1968 AN: 5156

South Asian (SAS) AF: 0.500 AC: 2408 AN: 4816

European-Finnish (FIN) AF: 0.463 AC: 4883 AN: 10540

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32754 AN: 67984

Other (OTH) AF: 0.491 AC: 1035 AN: 2108

Alfa AF: 0.492 Hom.: 59011

Bravo AF: 0.529

Asia WGS AF: 0.490 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.18
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;