16-77606335-A-G

Variant names:

• chr16-77606335-A-G
• rs13336488
• ENST00000563289.2:n.299-4202A>G

Variant summary

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

The ENST00000563289.2(LINC02131):​n.299-4202A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0596 in 151,770 control chromosomes in the GnomAD database, including 339 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 0.060 (339 hom., cov: 32)
• Consequence: LINC02131 ENST00000563289.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 1 publications found

Genes affected

LINC02131 (HGNC:52991): (long intergenic non-protein coding RNA 2131)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563289.2. 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
	LINC02131	NR_184319.1		n.196-4202A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02131	ENST00000563289.2	TSL:2	n.299-4202A>G		intron	N/A
	LINC02131	ENST00000731048.1		n.258-4202A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9038 AN: 151650 Hom.: 336 Cov.: 32

Gnomad AFR AF: 0.0828

Gnomad AMI AF: 0.00773

Gnomad AMR AF: 0.0578

Gnomad ASJ AF: 0.0200

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0379

Gnomad MID AF: 0.0256

Gnomad NFE AF: 0.0435

Gnomad OTH AF: 0.0432

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

GnomAD4 genome AF: 0.0596 AC: 9046 AN: 151770 Hom.: 339 Cov.: 32 AF XY: 0.0609 AC XY: 4517 AN XY: 74174

African (AFR) AF: 0.0826 AC: 3420 AN: 41382

American (AMR) AF: 0.0577 AC: 881 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0200 AC: 69 AN: 3458

East Asian (EAS) AF: 0.138 AC: 708 AN: 5126

South Asian (SAS) AF: 0.105 AC: 503 AN: 4794

European-Finnish (FIN) AF: 0.0379 AC: 401 AN: 10590

Middle Eastern (MID) AF: 0.0207 AC: 6 AN: 290

European-Non Finnish (NFE) AF: 0.0435 AC: 2950 AN: 67858

Other (OTH) AF: 0.0480 AC: 101 AN: 2104

Alfa AF: 0.0504 Hom.: 112

Bravo AF: 0.0619

Asia WGS AF: 0.169 AC: 586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.51
DANN	Benign	0.36
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs13336488; hg19: chr16-77640232;