rs10922924

Variant names:

• chr1-90787306-G-A
• rs10922924
• ENST00000435649.3:n.362+2092C>T

Variant summary

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

The ENST00000435649.3(LINC02609):​n.362+2092C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,932 control chromosomes in the GnomAD database, including 8,235 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 0.30 (8235 hom., cov: 32)
• Consequence: LINC02609 ENST00000435649.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 7 publications found

Genes affected

LINC02609 (HGNC:27140): (long intergenic non-protein coding RNA 2609)

ENSG00000287076 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02609	NR_135038.1	n.246+2092C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02609	ENST00000435649.3	n.362+2092C>T		intron_variant	Intron 2 of 2	5
LINC02609	ENST00000634619.2	n.738+2092C>T		intron_variant	Intron 4 of 4	5
LINC02609	ENST00000635581.4	n.543+2092C>T		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45361 AN: 151812 Hom.: 8238 Cov.: 32

Gnomad AFR AF: 0.0895

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.299 AC: 45368 AN: 151932 Hom.: 8235 Cov.: 32 AF XY: 0.302 AC XY: 22394 AN XY: 74238

African (AFR) AF: 0.0894 AC: 3707 AN: 41450

American (AMR) AF: 0.367 AC: 5596 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 922 AN: 3470

East Asian (EAS) AF: 0.193 AC: 998 AN: 5174

South Asian (SAS) AF: 0.345 AC: 1659 AN: 4812

European-Finnish (FIN) AF: 0.441 AC: 4642 AN: 10528

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26736 AN: 67920

Other (OTH) AF: 0.307 AC: 647 AN: 2108

Alfa AF: 0.357 Hom.: 33644

Bravo AF: 0.281

Asia WGS AF: 0.264 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.58
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs10922924; hg19: chr1-91252863;