chr2-66074959-G-A

Variant names:

• chr2-66074959-G-A
• rs2627857
• ENST00000606556.1:n.290+2307G>A

Variant summary

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

The ENST00000606556.1(LINC02934):​n.290+2307G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,928 control chromosomes in the GnomAD database, including 16,734 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 0.46 (16734 hom., cov: 31)
• Consequence: LINC02934 ENST00000606556.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 5 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606556.1. 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
	LINC02934	NR_187140.1		n.413+2307G>A		intron	N/A
	LINC02934	NR_187141.1		n.422+2307G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02934	ENST00000606556.1	TSL:2	n.290+2307G>A		intron	N/A
	LINC02934	ENST00000737096.1		n.346-9551G>A		intron	N/A
	LINC02934	ENST00000737097.1		n.559+2307G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70338 AN: 151812 Hom.: 16725 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.463 AC: 70386 AN: 151928 Hom.: 16734 Cov.: 31 AF XY: 0.457 AC XY: 33921 AN XY: 74224

African (AFR) AF: 0.375 AC: 15557 AN: 41442

American (AMR) AF: 0.428 AC: 6532 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1932 AN: 3472

East Asian (EAS) AF: 0.328 AC: 1684 AN: 5138

South Asian (SAS) AF: 0.363 AC: 1744 AN: 4802

European-Finnish (FIN) AF: 0.489 AC: 5155 AN: 10536

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 35993 AN: 67974

Other (OTH) AF: 0.502 AC: 1060 AN: 2112

Alfa AF: 0.508 Hom.: 85736

Bravo AF: 0.457

Asia WGS AF: 0.341 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.7
DANN	Benign	0.30
PhyloP100		1.4

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: rs2627857;

hg19: chr2-66302093;