rs10501761

Positions:

• chr11-91836654-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000671523.1(LINC02756):​n.312-2957G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02756	XR_001748324.2	n.709-2957G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02756	ENST00000671523.1	n.312-2957G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00328

Gnomad4 AMR AF: 0.0918

Gnomad4 ASJ AF: 0.00606

Gnomad4 EAS AF: 0.0490

Gnomad4 SAS AF: 0.0104

Gnomad4 FIN AF: 0.0248

Gnomad4 NFE AF: 0.0103

Gnomad4 OTH AF: 0.00947

Alfa AF: 0.0160 Hom.: 88

Bravo AF: 0.0227

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501761; hg19: chr11-91569820;