rs11236809

Variant names:

• chr11-76621166-T-G
• rs11236809
• ENST00000637683.1:n.1027+5407A>C

Variant summary

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

The ENST00000637683.1(LINC02757):​n.1027+5407A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0922 in 152,172 control chromosomes in the GnomAD database, including 957 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 0.092 (957 hom., cov: 31)
• Consequence: LINC02757 ENST00000637683.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.699
• Publications: 12 publications found

Genes affected

LINC02757 (HGNC:54277): (long intergenic non-protein coding RNA 2757)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) 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
LINC02757	NR_187241.1	n.310+7238A>C		intron_variant	Intron 2 of 2
LINC02757	NR_187242.1	n.1022+5407A>C		intron_variant	Intron 4 of 4
LINC02757	NR_187243.1	n.512+5407A>C		intron_variant	Intron 4 of 4
LINC02757	NR_187244.1	n.1126+4702A>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02757	ENST00000637683.1	n.1027+5407A>C		intron_variant	Intron 4 of 4	5
LINC02757	ENST00000656117.1	n.353+7238A>C		intron_variant	Intron 2 of 2
LINC02757	ENST00000716191.1	n.418+5407A>C		intron_variant	Intron 1 of 1
LINC02757	ENST00000716192.1	n.578+4702A>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0923 AC: 14035 AN: 152054 Hom.: 960 Cov.: 31

Gnomad AFR AF: 0.0213

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0932

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0922 AC: 14026 AN: 152172 Hom.: 957 Cov.: 31 AF XY: 0.0974 AC XY: 7244 AN XY: 74370

African (AFR) AF: 0.0213 AC: 885 AN: 41538

American (AMR) AF: 0.158 AC: 2420 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 363 AN: 3468

East Asian (EAS) AF: 0.262 AC: 1353 AN: 5164

South Asian (SAS) AF: 0.207 AC: 996 AN: 4816

European-Finnish (FIN) AF: 0.127 AC: 1340 AN: 10570

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0932 AC: 6339 AN: 68016

Other (OTH) AF: 0.0990 AC: 209 AN: 2112

Alfa AF: 0.0932 Hom.: 1466

Bravo AF: 0.0918

Asia WGS AF: 0.185 AC: 641 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.82
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs11236809; hg19: chr11-76332210;