9-106163108-A-G

Variant names:

• chr9-106163108-A-G
• rs4452860
• ENST00000637185.1:n.559+169240A>G

Variant summary

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

The ENST00000637185.1(LINC01505):​n.559+169240A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,128 control chromosomes in the GnomAD database, including 7,252 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 0.31 (7252 hom., cov: 32)
• Consequence: LINC01505 ENST00000637185.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524
• Publications: 11 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987108	XR_001746870.2	n.2032+186977A>G		intron_variant	Intron 3 of 5
LOC107987108	XR_007061713.1	n.2032+186977A>G		intron_variant	Intron 3 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01505	ENST00000637185.1	n.559+169240A>G		intron_variant	Intron 1 of 7	5

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46520 AN: 152010 Hom.: 7235 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.306 AC: 46573 AN: 152128 Hom.: 7252 Cov.: 32 AF XY: 0.307 AC XY: 22862 AN XY: 74384

African (AFR) AF: 0.339 AC: 14076 AN: 41480

American (AMR) AF: 0.289 AC: 4413 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1015 AN: 3470

East Asian (EAS) AF: 0.433 AC: 2235 AN: 5156

South Asian (SAS) AF: 0.190 AC: 914 AN: 4816

European-Finnish (FIN) AF: 0.320 AC: 3393 AN: 10590

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19582 AN: 68004

Other (OTH) AF: 0.296 AC: 627 AN: 2116

Alfa AF: 0.299 Hom.: 16383

Bravo AF: 0.306

Asia WGS AF: 0.273 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.48
DANN	Benign	0.67
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs4452860; hg19: chr9-108925389;