rs1729588

Positions:

• chr3-109588488-G-A
• chr3-109588488-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663929.1(LINC01205):​n.388-59067G>A variant causes a intron, non coding transcript 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 ENST00000663929.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01205	ENST00000663929.1	n.388-59067G>A		intron_variant, non_coding_transcript_variant
LINC01205	ENST00000658412.1	n.351-59067G>A		intron_variant, non_coding_transcript_variant
LINC01205	ENST00000659474.1	n.301+26229G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.331

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1729588; hg19: chr3-109307335;