rs1360806

Variant names:

• chr9-118689608-G-A
• rs1360806
• ENST00000450292.1:n.135-1605C>T

Variant summary

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

The ENST00000450292.1(ENSG00000225050):​n.135-1605C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 151,928 control chromosomes in the GnomAD database, including 4,857 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 0.25 (4857 hom., cov: 32)
• Consequence: ENSG00000225050 ENST00000450292.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664
• Publications: 3 publications found

Genes affected

ENSG00000225050 (HGNC:):

LINC02578 (HGNC:53750): (long intergenic non-protein coding RNA 2578)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02578	NR_151725.1	n.173+6363G>A		intron_variant	Intron 2 of 3
LOC102724929	XR_007061892.1	n.796-1605C>T		intron_variant	Intron 5 of 5
LOC102724929	XR_428592.5	n.177-1605C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225050	ENST00000450292.1	n.135-1605C>T		intron_variant	Intron 1 of 1	2
ENSG00000225050	ENST00000670605.2	n.562-1605C>T		intron_variant	Intron 2 of 2
ENSG00000225050	ENST00000819557.1	n.379-1605C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37586 AN: 151810 Hom.: 4859 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.247 AC: 37598 AN: 151928 Hom.: 4857 Cov.: 32 AF XY: 0.250 AC XY: 18551 AN XY: 74266

African (AFR) AF: 0.254 AC: 10520 AN: 41402

American (AMR) AF: 0.236 AC: 3602 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 896 AN: 3470

East Asian (EAS) AF: 0.453 AC: 2337 AN: 5162

South Asian (SAS) AF: 0.350 AC: 1687 AN: 4818

European-Finnish (FIN) AF: 0.235 AC: 2481 AN: 10556

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.227 AC: 15406 AN: 67934

Other (OTH) AF: 0.228 AC: 482 AN: 2112

Alfa AF: 0.241 Hom.: 4966

Bravo AF: 0.248

Asia WGS AF: 0.357 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.35
DANN	Benign	0.15
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs1360806; hg19: chr9-121451886;