2-65935278-T-C

Variant names:

• chr2-65935278-T-C
• rs7598978
• ENST00000606556.1:n.141+13209T>C

Variant summary

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

The ENST00000606556.1(LINC02934):​n.141+13209T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,050 control chromosomes in the GnomAD database, including 4,917 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 0.25 (4917 hom., cov: 32)
• Consequence: LINC02934 ENST00000606556.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.18
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02934	NR_187140.1	n.192+13209T>C		intron_variant	Intron 2 of 5
LINC02934	NR_187141.1	n.61-36270T>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02934	ENST00000606556.1	n.141+13209T>C		intron_variant	Intron 1 of 2	2
LINC02934	ENST00000606978.5	n.786+35969T>C		intron_variant	Intron 7 of 9	5

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38158 AN: 151930 Hom.: 4904 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.251 AC: 38203 AN: 152050 Hom.: 4917 Cov.: 32 AF XY: 0.257 AC XY: 19090 AN XY: 74312

African (AFR) AF: 0.236 AC: 9777 AN: 41486

American (AMR) AF: 0.239 AC: 3647 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 928 AN: 3472

East Asian (EAS) AF: 0.158 AC: 817 AN: 5170

South Asian (SAS) AF: 0.267 AC: 1287 AN: 4816

European-Finnish (FIN) AF: 0.361 AC: 3806 AN: 10556

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17155 AN: 67960

Other (OTH) AF: 0.238 AC: 503 AN: 2114

Alfa AF: 0.244 Hom.: 7997

Bravo AF: 0.239

Asia WGS AF: 0.230 AC: 801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0090
DANN	Benign	0.36
PhyloP100		-5.2

Splicing

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

Other links and lift over

dbSNP: rs7598978; hg19: chr2-66162412;