rs10501761

Variant names:

• chr11-91836654-G-A
• rs10501761
• ENST00000671523.1:n.312-2957G>A

Variant summary

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

The ENST00000671523.1(LINC02756):​n.312-2957G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0187 in 152,076 control chromosomes in the GnomAD database, including 96 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 0.019 (96 hom., cov: 32)
• Consequence: LINC02756 ENST00000671523.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 1 publications found

Genes affected

LINC02756 (HGNC:54276): (long intergenic non-protein coding RNA 2756)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0878 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671523.1. 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
	LINC02756	NR_187308.1		n.314-2957G>A		intron	N/A
	LINC02756	NR_187309.1		n.415-2957G>A		intron	N/A
	LINC02756	NR_187310.1		n.307-4931G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02756	ENST00000671523.1		n.312-2957G>A		intron	N/A
	LINC02756	ENST00000797231.1		n.172-19315G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0186 AC: 2834 AN: 151958 Hom.: 96 Cov.: 32

Gnomad AFR AF: 0.00328

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0915

Gnomad ASJ AF: 0.00606

Gnomad EAS AF: 0.0487

Gnomad SAS AF: 0.0102

Gnomad FIN AF: 0.0248

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0103

Gnomad OTH AF: 0.00957

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

GnomAD4 genome AF: 0.0187 AC: 2841 AN: 152076 Hom.: 96 Cov.: 32 AF XY: 0.0212 AC XY: 1579 AN XY: 74334

African (AFR) AF: 0.00328 AC: 136 AN: 41524

American (AMR) AF: 0.0918 AC: 1402 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00606 AC: 21 AN: 3468

East Asian (EAS) AF: 0.0490 AC: 250 AN: 5102

South Asian (SAS) AF: 0.0104 AC: 50 AN: 4822

European-Finnish (FIN) AF: 0.0248 AC: 263 AN: 10596

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0103 AC: 699 AN: 67970

Other (OTH) AF: 0.00947 AC: 20 AN: 2112

Alfa AF: 0.0165 Hom.: 117

Bravo AF: 0.0227

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.65
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs10501761; hg19: chr11-91569820;