rs17623128

Variant names:

• chr16-77596211-C-A
• rs17623128
• ENST00000563289.2:n.140-2874C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-77596211-C-A
• chr16-77596211-C-G
• chr16-77596211-C-T

Variant summary

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

The ENST00000563289.2(LINC02131):​n.140-2874C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,892 control chromosomes in the GnomAD database, including 8,153 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 0.31 (8153 hom., cov: 32)
• Consequence: LINC02131 ENST00000563289.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 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.37-2874C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02131	ENST00000563289.2	TSL:2	n.140-2874C>A		intron	N/A
	LINC02131	ENST00000731048.1		n.99-2874C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47718 AN: 151776 Hom.: 8151 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.314 AC: 47752 AN: 151892 Hom.: 8153 Cov.: 32 AF XY: 0.315 AC XY: 23353 AN XY: 74236

African (AFR) AF: 0.246 AC: 10188 AN: 41432

American (AMR) AF: 0.262 AC: 4006 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 885 AN: 3464

East Asian (EAS) AF: 0.630 AC: 3254 AN: 5164

South Asian (SAS) AF: 0.195 AC: 934 AN: 4800

European-Finnish (FIN) AF: 0.393 AC: 4135 AN: 10522

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23162 AN: 67934

Other (OTH) AF: 0.315 AC: 664 AN: 2108

Alfa AF: 0.218 Hom.: 757

Bravo AF: 0.310

Asia WGS AF: 0.375 AC: 1302 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.75
DANN	Benign	0.76
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs17623128; hg19: chr16-77630108;