9-106235833-C-T

Variant names:

• chr9-106235833-C-T
• rs12684013
• ENST00000637185.1:n.559+241965C>T

Variant summary

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

Score: -12 - Benign

-12

BP4_StrongBA1

The ENST00000637185.1(LINC01505):​n.559+241965C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,966 control chromosomes in the GnomAD database, including 4,920 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 0.23 (4920 hom., cov: 32)
• Consequence: LINC01505 ENST00000637185.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 8 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987108	XR_001746870.2	n.2032+259702C>T		intron_variant	Intron 3 of 5
LOC107987108	XR_007061713.1	n.2032+259702C>T		intron_variant	Intron 3 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01505	ENST00000637185.1	n.559+241965C>T		intron_variant	Intron 1 of 7	5

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35562 AN: 151846 Hom.: 4923 Cov.: 32

Gnomad AFR AF: 0.0969

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.234 AC: 35557 AN: 151966 Hom.: 4920 Cov.: 32 AF XY: 0.240 AC XY: 17790 AN XY: 74254

African (AFR) AF: 0.0967 AC: 4012 AN: 41510

American (AMR) AF: 0.262 AC: 3996 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 965 AN: 3470

East Asian (EAS) AF: 0.489 AC: 2514 AN: 5140

South Asian (SAS) AF: 0.161 AC: 776 AN: 4814

European-Finnish (FIN) AF: 0.352 AC: 3714 AN: 10546

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18772 AN: 67930

Other (OTH) AF: 0.242 AC: 510 AN: 2108

Alfa AF: 0.268 Hom.: 5910

Bravo AF: 0.224

Asia WGS AF: 0.250 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.7
DANN	Benign	0.39
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs12684013; hg19: chr9-108998114;