3-109597791-G-A

Variant names:

• chr3-109597791-G-A
• rs10511276
• ENST00000658412.1:n.351-49764G>A

Variant summary

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

The ENST00000658412.1(LINC01205):​n.351-49764G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,050 control chromosomes in the GnomAD database, including 7,978 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 0.32 (7978 hom., cov: 33)
• Consequence: LINC01205 ENST00000658412.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01
• Publications: 4 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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658412.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01205	ENST00000658412.1		n.351-49764G>A		intron	N/A
	LINC01205	ENST00000659474.1		n.301+35532G>A		intron	N/A
	LINC01205	ENST00000663929.1		n.388-49764G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48513 AN: 151930 Hom.: 7969 Cov.: 33

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.319 AC: 48539 AN: 152050 Hom.: 7978 Cov.: 33 AF XY: 0.317 AC XY: 23525 AN XY: 74324

African (AFR) AF: 0.329 AC: 13624 AN: 41436

American (AMR) AF: 0.274 AC: 4182 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3472

East Asian (EAS) AF: 0.182 AC: 940 AN: 5162

South Asian (SAS) AF: 0.429 AC: 2069 AN: 4820

European-Finnish (FIN) AF: 0.283 AC: 2990 AN: 10576

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22515 AN: 67986

Other (OTH) AF: 0.304 AC: 642 AN: 2114

Alfa AF: 0.325 Hom.: 32527

Bravo AF: 0.313

Asia WGS AF: 0.319 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.066
DANN	Benign	0.72
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs10511276; hg19: chr3-109316638;