3-150116202-G-T

Variant names:

• chr3-150116202-G-T
• rs4681577
• ENST00000472821.6:n.161-8736G>T

Variant summary

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

The ENST00000472821.6(LINC01213):​n.161-8736G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,034 control chromosomes in the GnomAD database, including 52,236 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 (52236 hom., cov: 30)
• Consequence: LINC01213 ENST00000472821.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 1 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000472821.6. 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
	LOC105374313	NR_136187.1		n.156-8736G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01213	ENST00000472821.6	TSL:3	n.161-8736G>T		intron	N/A
	LINC01213	ENST00000487840.6	TSL:2	n.99-8736G>T		intron	N/A
	LINC01213	ENST00000489690.1	TSL:3	n.120-8736G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124163 AN: 151914 Hom.: 52226 Cov.: 30

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.817 AC: 124214 AN: 152034 Hom.: 52236 Cov.: 30 AF XY: 0.818 AC XY: 60799 AN XY: 74332

African (AFR) AF: 0.616 AC: 25505 AN: 41426

American (AMR) AF: 0.852 AC: 13011 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3121 AN: 3472

East Asian (EAS) AF: 0.607 AC: 3130 AN: 5158

South Asian (SAS) AF: 0.868 AC: 4166 AN: 4802

European-Finnish (FIN) AF: 0.898 AC: 9505 AN: 10586

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.926 AC: 62969 AN: 68006

Other (OTH) AF: 0.836 AC: 1765 AN: 2110

Alfa AF: 0.889 Hom.: 17089

Bravo AF: 0.801

Asia WGS AF: 0.685 AC: 2387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.28
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs4681577; hg19: chr3-149833989;