ENST00000658412.1:n.351-59067G>A

Variant names:

• chr3-109588488-G-A
• rs1729588
• ENST00000658412.1:n.351-59067G>A

Variant summary

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

The ENST00000658412.1(LINC01205):​n.351-59067G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,760 control chromosomes in the GnomAD database, including 9,868 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 0.35 (9868 hom., cov: 32)
• Consequence: LINC01205 ENST00000658412.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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
LINC01205	ENST00000658412.1	n.351-59067G>A		intron_variant	Intron 3 of 4
LINC01205	ENST00000659474.1	n.301+26229G>A		intron_variant	Intron 4 of 5
LINC01205	ENST00000663929.1	n.388-59067G>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52730 AN: 151640 Hom.: 9869 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.348 AC: 52752 AN: 151760 Hom.: 9868 Cov.: 32 AF XY: 0.355 AC XY: 26342 AN XY: 74178

African (AFR) AF: 0.331 AC: 13715 AN: 41434

American (AMR) AF: 0.388 AC: 5915 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 895 AN: 3462

East Asian (EAS) AF: 0.754 AC: 3893 AN: 5166

South Asian (SAS) AF: 0.386 AC: 1857 AN: 4816

European-Finnish (FIN) AF: 0.409 AC: 4300 AN: 10520

Middle Eastern (MID) AF: 0.227 AC: 65 AN: 286

European-Non Finnish (NFE) AF: 0.313 AC: 21206 AN: 67808

Other (OTH) AF: 0.331 AC: 697 AN: 2108

Alfa AF: 0.336 Hom.: 1114

Bravo AF: 0.345

Asia WGS AF: 0.545 AC: 1864 AN: 3422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.40
DANN	Benign	0.67
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1729588; hg19: chr3-109307335;