chr2-65940430-G-A

Variant names:

• chr2-65940430-G-A
• rs1549383
• ENST00000606556.1:n.141+18361G>A

Variant summary

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

The ENST00000606556.1(LINC02934):​n.141+18361G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,892 control chromosomes in the GnomAD database, including 8,427 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 0.33 (8427 hom., cov: 32)
• Consequence: LINC02934 ENST00000606556.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02934	NR_187140.1	n.192+18361G>A		intron_variant	Intron 2 of 5
LINC02934	NR_187141.1	n.61-31118G>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02934	ENST00000606556.1	n.141+18361G>A		intron_variant	Intron 1 of 2	2
LINC02934	ENST00000606978.5	n.787-31118G>A		intron_variant	Intron 7 of 9	5

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49737 AN: 151774 Hom.: 8410 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.328 AC: 49792 AN: 151892 Hom.: 8427 Cov.: 32 AF XY: 0.331 AC XY: 24557 AN XY: 74226

African (AFR) AF: 0.273 AC: 11322 AN: 41406

American (AMR) AF: 0.428 AC: 6536 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 977 AN: 3466

East Asian (EAS) AF: 0.534 AC: 2756 AN: 5164

South Asian (SAS) AF: 0.338 AC: 1624 AN: 4810

European-Finnish (FIN) AF: 0.321 AC: 3380 AN: 10520

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.328 AC: 22256 AN: 67946

Other (OTH) AF: 0.330 AC: 696 AN: 2106

Alfa AF: 0.327 Hom.: 1622

Bravo AF: 0.334

Asia WGS AF: 0.429 AC: 1493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.59
DANN	Benign	0.44
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs1549383; hg19: chr2-66167564;