chr2-65705283-T-C

Variant names:

• chr2-65705283-T-C
• rs2860851
• ENST00000606978.5:n.633+13324T>C

Variant summary

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

The ENST00000822260.1(LINC02934):​n.545+13324T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0514 in 152,130 control chromosomes in the GnomAD database, including 372 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 0.051 (372 hom., cov: 32)
• Consequence: LINC02934 ENST00000822260.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000822260.1. 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
	LINC02934	ENST00000606978.5	TSL:5	n.633+13324T>C		intron	N/A
	LINC02934	ENST00000822260.1		n.545+13324T>C		intron	N/A
	LINC02934	ENST00000822283.1		n.216+13324T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0514 AC: 7807 AN: 152012 Hom.: 372 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0577

Gnomad ASJ AF: 0.00865

Gnomad EAS AF: 0.0990

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0113

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0138

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0514 AC: 7814 AN: 152130 Hom.: 372 Cov.: 32 AF XY: 0.0520 AC XY: 3868 AN XY: 74400

African (AFR) AF: 0.112 AC: 4631 AN: 41486

American (AMR) AF: 0.0577 AC: 882 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00865 AC: 30 AN: 3470

East Asian (EAS) AF: 0.0983 AC: 509 AN: 5180

South Asian (SAS) AF: 0.124 AC: 595 AN: 4816

European-Finnish (FIN) AF: 0.0113 AC: 120 AN: 10608

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0138 AC: 939 AN: 67972

Other (OTH) AF: 0.0464 AC: 98 AN: 2112

Alfa AF: 0.0271 Hom.: 29

Bravo AF: 0.0572

Asia WGS AF: 0.123 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.77
DANN	Benign	0.55
PhyloP100		-0.020
Mutation Taster		=100/0	polymorphism

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: rs2860851;

hg19: chr2-65932417;