3-109485566-C-T

Variant names:

• chr3-109485566-C-T
• rs769554
• ENST00000497996.1:n.465-8573C>T

Variant summary

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

The ENST00000497996.1(LINC01205):​n.465-8573C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0179 in 152,048 control chromosomes in the GnomAD database, including 83 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 0.018 (83 hom., cov: 32)
• Consequence: LINC01205 ENST00000497996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 7 publications found

Genes affected

LINC01205 (HGNC:49636): (long intergenic non-protein coding RNA 1205)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01205	NR_109841.1	n.465-8573C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01205	ENST00000497996.1	n.465-8573C>T		intron_variant	Intron 4 of 4	2
LINC01205	ENST00000658412.1	n.350+25638C>T		intron_variant	Intron 3 of 4
LINC01205	ENST00000659474.1	n.273+25638C>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.0179 AC: 2722 AN: 151930 Hom.: 84 Cov.: 32

Gnomad AFR AF: 0.0624

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00584

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.000945

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.000147

Gnomad OTH AF: 0.0124

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

GnomAD4 genome AF: 0.0179 AC: 2724 AN: 152048 Hom.: 83 Cov.: 32 AF XY: 0.0176 AC XY: 1307 AN XY: 74326

African (AFR) AF: 0.0623 AC: 2586 AN: 41500

American (AMR) AF: 0.00583 AC: 89 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4814

European-Finnish (FIN) AF: 0.000945 AC: 10 AN: 10580

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.000147 AC: 10 AN: 67930

Other (OTH) AF: 0.0123 AC: 26 AN: 2112

Alfa AF: 0.00772 Hom.: 50

Bravo AF: 0.0202

Asia WGS AF: 0.00231 AC: 9 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.4
DANN	Benign	0.60
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs769554; hg19: chr3-109204413;