rs1766167

Variant names:

• chr1-90836250-A-G
• rs1766167
• ENST00000670363.1:n.179T>C

Variant summary

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

The ENST00000670363.1(LINC02609):​n.179T>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 0.281 in 152,138 control chromosomes in the GnomAD database, including 6,205 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 0.28 (6202 hom., cov: 33)
  • Exomes 𝑓: 0.42 (3 hom.)
• Consequence: LINC02609 ENST00000670363.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 2 publications found

Genes affected

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

LINC02788 (HGNC:54309): (long intergenic non-protein coding RNA 2788)

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 = 0.353 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670363.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02609	NR_135038.1		n.156+15233T>C		intron	N/A
	LINC02609	NR_147930.1		n.169-4054T>C		intron	N/A
	LINC02609	NR_147931.1		n.384+1300T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02609	ENST00000670363.1		n.179T>C		non_coding_transcript_exon	Exon 1 of 2
	LINC02609	ENST00000670437.2		n.124T>C		non_coding_transcript_exon	Exon 1 of 2
	LINC02609	ENST00000443802.4	TSL:3	n.405+1300T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42690 AN: 151998 Hom.: 6205 Cov.: 33

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.292

GnomAD4 exome AF: 0.417 AC: 10 AN: 24 Hom.: 3 AF XY: 0.450 AC XY: 9 AN XY: 20

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.455 AC: 10 AN: 22

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.281 AC: 42700 AN: 152114 Hom.: 6202 Cov.: 33 AF XY: 0.280 AC XY: 20787 AN XY: 74352

African (AFR) AF: 0.315 AC: 13086 AN: 41514

American (AMR) AF: 0.249 AC: 3810 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1393 AN: 3470

East Asian (EAS) AF: 0.367 AC: 1883 AN: 5130

South Asian (SAS) AF: 0.324 AC: 1565 AN: 4828

European-Finnish (FIN) AF: 0.186 AC: 1968 AN: 10600

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.266 AC: 18067 AN: 67962

Other (OTH) AF: 0.291 AC: 616 AN: 2114

Alfa AF: 0.272 Hom.: 9978

Bravo AF: 0.288

Asia WGS AF: 0.311 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.20
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1766167; hg19: chr1-91301807;