2-65532537-A-G

Variant names:

• chr2-65532537-A-G
• rs3911862
• ENST00000377977.3:n.862+31390A>G

Variant summary

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

The ENST00000377977.3(LINC02934):​n.862+31390A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,070 control chromosomes in the GnomAD database, including 19,696 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 0.50 (19696 hom., cov: 32)
• Consequence: LINC02934 ENST00000377977.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338
• Publications: 6 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=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000377977.3. 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
	LINC02934	ENST00000377977.3	TSL:2	n.862+31390A>G		intron	N/A
	LINC02934	ENST00000606978.5	TSL:5	n.455+49385A>G		intron	N/A
	LINC02934	ENST00000661422.1		n.2253-18715A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76157 AN: 151952 Hom.: 19696 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.501 AC: 76166 AN: 152070 Hom.: 19696 Cov.: 32 AF XY: 0.506 AC XY: 37645 AN XY: 74342

African (AFR) AF: 0.368 AC: 15264 AN: 41476

American (AMR) AF: 0.546 AC: 8347 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1536 AN: 3470

East Asian (EAS) AF: 0.613 AC: 3172 AN: 5178

South Asian (SAS) AF: 0.662 AC: 3187 AN: 4816

European-Finnish (FIN) AF: 0.562 AC: 5926 AN: 10552

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37166 AN: 67974

Other (OTH) AF: 0.471 AC: 996 AN: 2116

Alfa AF: 0.523 Hom.: 67067

Bravo AF: 0.489

Asia WGS AF: 0.630 AC: 2187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.7
DANN	Benign	0.77
PhyloP100		0.34

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: rs3911862;

hg19: chr2-65759671;