chr1-90848953-T-C

Variant names:

• chr1-90848953-T-C
• rs1766163
• ENST00000443802.4:n.189+2530A>G

Variant summary

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

The ENST00000606660.1(LINC02609):​n.136+2530A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,940 control chromosomes in the GnomAD database, including 22,132 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 0.54 (22132 hom., cov: 32)
• Consequence: LINC02609 ENST00000606660.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02609	NR_135038.1	n.156+2530A>G		intron_variant	Intron 1 of 2
LINC02609	NR_147930.1	n.168+2530A>G		intron_variant	Intron 1 of 1
LINC02609	NR_147931.1	n.168+2530A>G		intron_variant	Intron 1 of 2
LINC02788	NR_186594.1	n.470-36T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02609	ENST00000443802.4	n.189+2530A>G		intron_variant	Intron 1 of 2	3
LINC02609	ENST00000606660.1	n.136+2530A>G		intron_variant	Intron 1 of 1	2
LINC02609	ENST00000634619.2	n.165+2530A>G		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81565 AN: 151822 Hom.: 22126 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.537 AC: 81623 AN: 151940 Hom.: 22132 Cov.: 32 AF XY: 0.538 AC XY: 39926 AN XY: 74276

African (AFR) AF: 0.501 AC: 20736 AN: 41418

American (AMR) AF: 0.531 AC: 8112 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2270 AN: 3464

East Asian (EAS) AF: 0.770 AC: 3982 AN: 5174

South Asian (SAS) AF: 0.630 AC: 3028 AN: 4808

European-Finnish (FIN) AF: 0.487 AC: 5125 AN: 10534

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36607 AN: 67956

Other (OTH) AF: 0.547 AC: 1156 AN: 2114

Alfa AF: 0.536 Hom.: 14499

Bravo AF: 0.539

Asia WGS AF: 0.663 AC: 2307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.73
PhyloP100		-0.55

Splicing

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

Publications

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Other links and lift over

dbSNP: rs1766163; hg19: chr1-91314510;