rs6757749

Variant names:

• chr2-826147-G-A
• rs6757749
• ENST00000415700.2:n.153-19898C>T

Variant summary

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

The ENST00000415700.2(LINC01115):​n.153-19898C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,954 control chromosomes in the GnomAD database, including 4,192 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 0.23 (4192 hom., cov: 32)
• Consequence: LINC01115 ENST00000415700.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 2 publications found

Genes affected

LINC01115 (HGNC:49258): (long intergenic non-protein coding RNA 1115)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01115	NR_033880.3	n.547-19898C>T		intron_variant	Intron 2 of 3
LINC01115	NR_111963.1	n.310-19898C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01115	ENST00000415700.2	n.153-19898C>T		intron_variant	Intron 1 of 2	1
LINC01115	ENST00000621134.4	n.547-19898C>T		intron_variant	Intron 2 of 3	1
LINC01115	ENST00000648115.1	n.492-19898C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35439 AN: 151836 Hom.: 4190 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.233 AC: 35457 AN: 151954 Hom.: 4192 Cov.: 32 AF XY: 0.229 AC XY: 16987 AN XY: 74266

African (AFR) AF: 0.231 AC: 9577 AN: 41408

American (AMR) AF: 0.168 AC: 2563 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 933 AN: 3470

East Asian (EAS) AF: 0.178 AC: 918 AN: 5166

South Asian (SAS) AF: 0.179 AC: 863 AN: 4824

European-Finnish (FIN) AF: 0.256 AC: 2698 AN: 10540

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17200 AN: 67958

Other (OTH) AF: 0.217 AC: 456 AN: 2106

Alfa AF: 0.248 Hom.: 6031

Bravo AF: 0.228

Asia WGS AF: 0.174 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs6757749; hg19: chr2-822116;