chr2-65809406-G-A

Variant names:

• chr2-65809406-G-A
• rs3919602
• ENST00000412986.2:n.53+19272G>A

Variant summary

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

The ENST00000412986.2(LINC02934):​n.53+19272G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,092 control chromosomes in the GnomAD database, including 4,486 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 0.22 (4486 hom., cov: 32)
• Consequence: LINC02934 ENST00000412986.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144
• Publications: 4 publications found

Genes affected

LINC02934 (HGNC:55913): (long intergenic non-protein coding RNA 2934)

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 (AMR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412986.2. 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
	LINC02934	NR_187140.1		n.60+19272G>A		intron	N/A
	LINC02934	NR_187141.1		n.60+19272G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02934	ENST00000412986.2	TSL:2	n.53+19272G>A		intron	N/A
	LINC02934	ENST00000606978.5	TSL:5	n.668+54623G>A		intron	N/A
	LINC02934	ENST00000793166.1		n.43+19272G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33537 AN: 151972 Hom.: 4488 Cov.: 32

Gnomad AFR AF: 0.0646

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.221 AC: 33537 AN: 152092 Hom.: 4486 Cov.: 32 AF XY: 0.218 AC XY: 16230 AN XY: 74330

African (AFR) AF: 0.0645 AC: 2678 AN: 41528

American (AMR) AF: 0.303 AC: 4632 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1262 AN: 3470

East Asian (EAS) AF: 0.280 AC: 1441 AN: 5154

South Asian (SAS) AF: 0.173 AC: 835 AN: 4824

European-Finnish (FIN) AF: 0.252 AC: 2666 AN: 10560

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19177 AN: 67972

Other (OTH) AF: 0.233 AC: 491 AN: 2110

Alfa AF: 0.258 Hom.: 12306

Bravo AF: 0.220

Asia WGS AF: 0.209 AC: 725 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	1.4
DANN	Benign	0.81
PhyloP100		0.14

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: rs3919602;

hg19: chr2-66036540;