rs1023849

Variant names:

• chr11-96856557-C-G
• rs1023849
• ENST00000716809.1:n.241+73319C>G

Variant summary

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

The ENST00000716809.1(LINC02737):​n.241+73319C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,654 control chromosomes in the GnomAD database, including 8,024 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 0.30 (8024 hom., cov: 32)
• Consequence: LINC02737 ENST00000716809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 0 publications found

Genes affected

LINC02737 (HGNC:54254): (long intergenic non-protein coding RNA 2737)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 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
LINC02737	ENST00000716809.1	n.241+73319C>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45621 AN: 151534 Hom.: 8022 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.301 AC: 45634 AN: 151654 Hom.: 8024 Cov.: 32 AF XY: 0.300 AC XY: 22259 AN XY: 74114

African (AFR) AF: 0.127 AC: 5259 AN: 41458

American (AMR) AF: 0.341 AC: 5178 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1145 AN: 3468

East Asian (EAS) AF: 0.156 AC: 804 AN: 5160

South Asian (SAS) AF: 0.285 AC: 1373 AN: 4818

European-Finnish (FIN) AF: 0.441 AC: 4645 AN: 10536

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.387 AC: 26209 AN: 67734

Other (OTH) AF: 0.260 AC: 547 AN: 2102

Alfa AF: 0.342 Hom.: 1214

Bravo AF: 0.282

Asia WGS AF: 0.213 AC: 743 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
DANN	Benign	0.79
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1023849; hg19: chr11-96727557;