rs2954963

Variant names:

• chr2-66192552-G-A
• rs2954963
• ENST00000666114.1:n.347-6662G>A

Variant summary

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

The ENST00000666114.1(LINC02934):​n.347-6662G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 151,840 control chromosomes in the GnomAD database, including 7,103 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 0.29 (7103 hom., cov: 32)
• Consequence: LINC02934 ENST00000666114.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.732
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02934	ENST00000666114.1	n.347-6662G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43447 AN: 151722 Hom.: 7086 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.287 AC: 43509 AN: 151840 Hom.: 7103 Cov.: 32 AF XY: 0.282 AC XY: 20892 AN XY: 74192

African (AFR) AF: 0.438 AC: 18122 AN: 41354

American (AMR) AF: 0.269 AC: 4105 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1080 AN: 3464

East Asian (EAS) AF: 0.237 AC: 1222 AN: 5160

South Asian (SAS) AF: 0.145 AC: 696 AN: 4808

European-Finnish (FIN) AF: 0.175 AC: 1841 AN: 10528

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.227 AC: 15426 AN: 67954

Other (OTH) AF: 0.292 AC: 614 AN: 2100

Alfa AF: 0.261 Hom.: 1019

Bravo AF: 0.301

Asia WGS AF: 0.208 AC: 723 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	6.0
DANN	Benign	0.39
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs2954963; hg19: chr2-66419684; COSMIC: COSV71060279;