chr2-32896437-A-G

Variant names:

• chr2-32896437-A-G
• rs6728021
• ENST00000435075.1:n.27-2103A>G

Variant summary

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

The ENST00000435075.1(LINC00486):​n.27-2103A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0776 in 152,180 control chromosomes in the GnomAD database, including 544 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 0.078 (544 hom., cov: 32)
• Consequence: LINC00486 ENST00000435075.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.569
• Publications: 8 publications found

Genes affected

LINC00486 (HGNC:42946): (long intergenic non-protein coding RNA 486)

ENSG00000293668 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435075.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00486	ENST00000435075.1	TSL:1	n.27-2103A>G		intron	N/A
	LINC00486	ENST00000414054.5	TSL:4	n.290-2103A>G		intron	N/A
	LINC00486	ENST00000424364.6	TSL:5	n.473-488A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0776 AC: 11799 AN: 152062 Hom.: 544 Cov.: 32

Gnomad AFR AF: 0.0428

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0622

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0150

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0776 AC: 11808 AN: 152180 Hom.: 544 Cov.: 32 AF XY: 0.0753 AC XY: 5603 AN XY: 74414

African (AFR) AF: 0.0429 AC: 1783 AN: 41528

American (AMR) AF: 0.0622 AC: 951 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 393 AN: 3470

East Asian (EAS) AF: 0.00290 AC: 15 AN: 5174

South Asian (SAS) AF: 0.0150 AC: 72 AN: 4810

European-Finnish (FIN) AF: 0.0753 AC: 798 AN: 10598

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7482 AN: 67984

Other (OTH) AF: 0.0705 AC: 149 AN: 2114

Alfa AF: 0.0970 Hom.: 3368

Bravo AF: 0.0759

Asia WGS AF: 0.0130 AC: 46 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.85
PhyloP100		0.57

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6728021;

hg19: chr2-33121504;