rs2029206

Variant names:

• chr3-150124050-A-G
• rs2029206
• ENST00000472821.6:n.161-888A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-150124050-A-G
• chr3-150124050-A-T

Variant summary

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

The ENST00000487840.6(LINC01213):​n.99-888A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 152,192 control chromosomes in the GnomAD database, including 52,198 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 0.82 (52198 hom., cov: 32)
• Consequence: LINC01213 ENST00000487840.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 3 publications found

Genes affected

LINC01213 (HGNC:49648): (long intergenic non-protein coding RNA 1213)

LOC105374313 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000487840.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105374313	NR_136187.1		n.156-888A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01213	ENST00000472821.6	TSL:3	n.161-888A>G		intron	N/A
	LINC01213	ENST00000487840.6	TSL:2	n.99-888A>G		intron	N/A
	LINC01213	ENST00000489690.1	TSL:3	n.120-888A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125402 AN: 152074 Hom.: 52162 Cov.: 32

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.825 AC: 125490 AN: 152192 Hom.: 52198 Cov.: 32 AF XY: 0.823 AC XY: 61217 AN XY: 74410

African (AFR) AF: 0.938 AC: 38979 AN: 41542

American (AMR) AF: 0.848 AC: 12965 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2812 AN: 3472

East Asian (EAS) AF: 0.671 AC: 3469 AN: 5172

South Asian (SAS) AF: 0.768 AC: 3698 AN: 4812

European-Finnish (FIN) AF: 0.752 AC: 7969 AN: 10594

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52846 AN: 68000

Other (OTH) AF: 0.824 AC: 1741 AN: 2112

Alfa AF: 0.793 Hom.: 24536

Bravo AF: 0.838

Asia WGS AF: 0.731 AC: 2545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-0.31

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2029206;

hg19: chr3-149841837;