2-7955027-A-G

Variant names:

• chr2-7955027-A-G
• rs41009
• ENST00000426969.5:n.312+13118T>C

Variant summary

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

The ENST00000426969.5(LINC00299):​n.312+13118T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,176 control chromosomes in the GnomAD database, including 41,214 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 0.68 (41214 hom., cov: 33)
• Consequence: LINC00299 ENST00000426969.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183
• Publications: 6 publications found

Genes affected

LINC00299 (HGNC:27940): (long intergenic non-protein coding RNA 299)

LINC00298 (HGNC:49257): (long intergenic non-protein coding RNA 298)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00298	NR_015405.1	n.241+13118T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00299	ENST00000426969.5	n.312+13118T>C		intron_variant	Intron 3 of 3	1
LINC00299	ENST00000456681.1	n.551+21682T>C		intron_variant	Intron 3 of 3	3
LINC00299	ENST00000663636.1	n.788+13118T>C		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103559 AN: 152058 Hom.: 41213 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.681 AC: 103570 AN: 152176 Hom.: 41214 Cov.: 33 AF XY: 0.683 AC XY: 50837 AN XY: 74396

African (AFR) AF: 0.231 AC: 9582 AN: 41512

American (AMR) AF: 0.833 AC: 12742 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2786 AN: 3472

East Asian (EAS) AF: 0.843 AC: 4351 AN: 5164

South Asian (SAS) AF: 0.809 AC: 3904 AN: 4826

European-Finnish (FIN) AF: 0.842 AC: 8920 AN: 10592

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.863 AC: 58680 AN: 68002

Other (OTH) AF: 0.733 AC: 1549 AN: 2112

Alfa AF: 0.774 Hom.: 95812

Bravo AF: 0.662

Asia WGS AF: 0.784 AC: 2729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.98
DANN	Benign	0.83
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs41009; hg19: chr2-8095158;