chr3-13701633-G-T

Variant names:

• chr3-13701633-G-T
• rs9846232
• ENST00000419618.2:n.217+13417G>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+13417G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0489 in 152,296 control chromosomes in the GnomAD database, including 434 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 0.049 (434 hom., cov: 33)
• Consequence: LINC00620 ENST00000419618.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 8 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00620	NR_027103.1		n.217+13417G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00620	ENST00000419618.2	TSL:1	n.217+13417G>T		intron	N/A
	LINC00620	ENST00000438915.2	TSL:4	n.203-44611G>T		intron	N/A
	LINC00620	ENST00000665476.1		n.205+13417G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0487 AC: 7415 AN: 152178 Hom.: 436 Cov.: 33

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.0398

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.00352

Gnomad FIN AF: 0.00584

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.00985

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0489 AC: 7442 AN: 152296 Hom.: 434 Cov.: 33 AF XY: 0.0478 AC XY: 3560 AN XY: 74480

African (AFR) AF: 0.141 AC: 5868 AN: 41546

American (AMR) AF: 0.0355 AC: 543 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0398 AC: 138 AN: 3468

East Asian (EAS) AF: 0.00173 AC: 9 AN: 5192

South Asian (SAS) AF: 0.00331 AC: 16 AN: 4828

European-Finnish (FIN) AF: 0.00584 AC: 62 AN: 10614

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.00985 AC: 670 AN: 68018

Other (OTH) AF: 0.0539 AC: 114 AN: 2116

Alfa AF: 0.0221 Hom.: 484

Bravo AF: 0.0564

Asia WGS AF: 0.0240 AC: 84 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	0.57
DANN	Benign	0.48
PhyloP100		-0.38
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: rs9846232; hg19: chr3-13743132;