1-90781472-T-G

Variant names:

• chr1-90781472-T-G
• rs3856228
• ENST00000659034.4:n.2231A>C

Variant summary

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

The ENST00000659034.4(LINC02609):​n.2231A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,838 control chromosomes in the GnomAD database, including 8,319 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 (8319 hom., cov: 31)
• Consequence: LINC02609 ENST00000659034.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.680
• Publications: 2 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=-0.73).
• 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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02609	ENST00000659034.4	n.2231A>C		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02609	ENST00000671059.1	n.136+7926A>C		intron_variant	Intron 2 of 2
ENSG00000287076	ENST00000759598.1	n.369+150T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45755 AN: 151722 Hom.: 8323 Cov.: 31

Gnomad AFR AF: 0.0902

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.301 AC: 45756 AN: 151838 Hom.: 8319 Cov.: 31 AF XY: 0.305 AC XY: 22605 AN XY: 74178

African (AFR) AF: 0.0902 AC: 3741 AN: 41496

American (AMR) AF: 0.368 AC: 5609 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 921 AN: 3470

East Asian (EAS) AF: 0.259 AC: 1335 AN: 5150

South Asian (SAS) AF: 0.351 AC: 1684 AN: 4800

European-Finnish (FIN) AF: 0.442 AC: 4640 AN: 10486

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.394 AC: 26713 AN: 67882

Other (OTH) AF: 0.311 AC: 656 AN: 2112

Alfa AF: 0.366 Hom.: 4981

Bravo AF: 0.285

Asia WGS AF: 0.287 AC: 999 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.5
DANN	Benign	0.69
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs3856228; hg19: chr1-91247029;