chr2-66058737-T-C

Variant names:

• chr2-66058737-T-C
• rs4671709
• ENST00000606556.1:n.142-13767T>C

Variant summary

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

The ENST00000606556.1(LINC02934):​n.142-13767T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 152,042 control chromosomes in the GnomAD database, including 19,990 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 0.51 (19990 hom., cov: 32)
• Consequence: LINC02934 ENST00000606556.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02934	NR_187140.1	n.265-13767T>C		intron_variant	Intron 3 of 5
LINC02934	NR_187141.1	n.274-13767T>C		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02934	ENST00000606556.1	n.142-13767T>C		intron_variant	Intron 1 of 2	2
LINC02934	ENST00000606978.5	n.1000-13767T>C		intron_variant	Intron 9 of 9	5
LINC02934	ENST00000737096.1	n.346-25773T>C		intron_variant	Intron 2 of 5
LINC02934	ENST00000737097.1	n.410+8883T>C		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77653 AN: 151924 Hom.: 19966 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.511 AC: 77728 AN: 152042 Hom.: 19990 Cov.: 32 AF XY: 0.514 AC XY: 38208 AN XY: 74316

African (AFR) AF: 0.490 AC: 20313 AN: 41480

American (AMR) AF: 0.548 AC: 8366 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1847 AN: 3470

East Asian (EAS) AF: 0.545 AC: 2807 AN: 5152

South Asian (SAS) AF: 0.513 AC: 2474 AN: 4826

European-Finnish (FIN) AF: 0.545 AC: 5758 AN: 10564

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34622 AN: 67960

Other (OTH) AF: 0.504 AC: 1064 AN: 2112

Alfa AF: 0.511 Hom.: 52818

Bravo AF: 0.510

Asia WGS AF: 0.562 AC: 1955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.6
DANN	Benign	0.80
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs4671709; hg19: chr2-66285871;