chr2-65921332-A-G

Variant names:

• chr2-65921332-A-G
• rs6728803
• ENST00000606978.5:n.786+22023A>G

Variant summary

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

The ENST00000606978.5(LINC02934):​n.786+22023A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 152,078 control chromosomes in the GnomAD database, including 30,840 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 0.62 (30840 hom., cov: 32)
• Consequence: LINC02934 ENST00000606978.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02934	NR_187140.1	n.61-606A>G		intron_variant	Intron 1 of 5
LINC02934	NR_187141.1	n.61-50216A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02934	ENST00000606978.5	n.786+22023A>G		intron_variant	Intron 7 of 9	5

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93523 AN: 151960 Hom.: 30785 Cov.: 32

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.616 AC: 93639 AN: 152078 Hom.: 30840 Cov.: 32 AF XY: 0.620 AC XY: 46112 AN XY: 74324

African (AFR) AF: 0.863 AC: 35818 AN: 41516

American (AMR) AF: 0.585 AC: 8938 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1602 AN: 3468

East Asian (EAS) AF: 0.723 AC: 3738 AN: 5168

South Asian (SAS) AF: 0.631 AC: 3041 AN: 4816

European-Finnish (FIN) AF: 0.553 AC: 5836 AN: 10558

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33050 AN: 67962

Other (OTH) AF: 0.552 AC: 1165 AN: 2110

Alfa AF: 0.528 Hom.: 71060

Bravo AF: 0.626

Asia WGS AF: 0.683 AC: 2374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.55
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs6728803; hg19: chr2-66148466;