3-13699088-G-T

Variant names:

• chr3-13699088-G-T
• rs9830807
• ENST00000419618.2:n.217+10872G>T

Variant summary

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

The ENST00000419618.2(LINC00620):​n.217+10872G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 84,870 control chromosomes in the GnomAD database, including 1,760 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 0.16 (1760 hom., cov: 34)
• Consequence: LINC00620 ENST00000419618.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369
• Publications: 1 publications found

Genes affected

LINC00620 (HGNC:44223): (long intergenic non-protein coding RNA 620)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419618.2. 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
	LINC00620	NR_027103.1		n.217+10872G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00620	ENST00000419618.2	TSL:1	n.217+10872G>T		intron	N/A
	LINC00620	ENST00000438915.2	TSL:4	n.203-47156G>T		intron	N/A
	LINC00620	ENST00000665476.1		n.205+10872G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.161 AC: 13682 AN: 84768 Hom.: 1744 Cov.: 34

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.0605

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0650

Gnomad EAS AF: 0.00340

Gnomad SAS AF: 0.0133

Gnomad FIN AF: 0.0143

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.0193

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.162 AC: 13744 AN: 84870 Hom.: 1760 Cov.: 34 AF XY: 0.165 AC XY: 6596 AN XY: 39910

African (AFR) AF: 0.411 AC: 11806 AN: 28694

American (AMR) AF: 0.111 AC: 771 AN: 6960

Ashkenazi Jewish (ASJ) AF: 0.0650 AC: 139 AN: 2138

East Asian (EAS) AF: 0.00341 AC: 8 AN: 2348

South Asian (SAS) AF: 0.0121 AC: 18 AN: 1490

European-Finnish (FIN) AF: 0.0143 AC: 62 AN: 4346

Middle Eastern (MID) AF: 0.121 AC: 22 AN: 182

European-Non Finnish (NFE) AF: 0.0193 AC: 716 AN: 37174

Other (OTH) AF: 0.165 AC: 172 AN: 1042

Alfa AF: 0.0498 Hom.: 309

Bravo AF: 0.104

Asia WGS AF: 0.0250 AC: 86 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.53
PhyloP100		0.37
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs9830807; hg19: chr3-13740587;