rs4938265

Variant names:

• chr11-116394628-C-G
• rs4938265
• ENST00000815587.1:n.239-74189G>C

Variant summary

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

The ENST00000815587.1(LINC02151):​n.239-74189G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,138 control chromosomes in the GnomAD database, including 1,805 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 0.11 (1805 hom., cov: 32)
• Consequence: LINC02151 ENST00000815587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738
• Publications: 1 publications found

Genes affected

LINC02151 (HGNC:53013): (long intergenic non-protein coding RNA 2151)

ENSG00000306159 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815587.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02151	ENST00000815587.1		n.239-74189G>C		intron	N/A
	LINC02151	ENST00000815588.1		n.201+26108G>C		intron	N/A
	ENSG00000306159	ENST00000815711.1		n.162+3262C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16018 AN: 152020 Hom.: 1804 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0979

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.0723

Gnomad SAS AF: 0.0529

Gnomad FIN AF: 0.0633

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0166

Gnomad OTH AF: 0.0920

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

GnomAD4 genome AF: 0.105 AC: 16040 AN: 152138 Hom.: 1805 Cov.: 32 AF XY: 0.105 AC XY: 7800 AN XY: 74372

African (AFR) AF: 0.282 AC: 11713 AN: 41466

American (AMR) AF: 0.0983 AC: 1503 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0545 AC: 189 AN: 3470

East Asian (EAS) AF: 0.0724 AC: 375 AN: 5176

South Asian (SAS) AF: 0.0526 AC: 253 AN: 4812

European-Finnish (FIN) AF: 0.0633 AC: 671 AN: 10598

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0166 AC: 1129 AN: 68012

Other (OTH) AF: 0.0906 AC: 191 AN: 2108

Alfa AF: 0.0686 Hom.: 148

Bravo AF: 0.119

Asia WGS AF: 0.0810 AC: 283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.9
DANN	Benign	0.47
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs4938265; hg19: chr11-116265345;