rs11088971

Variant names:

• chr21-44935795-A-C
• rs11088971
• ENST00000330551.3:n.493T>G

Your query was ambiguous. Multiple possible variants found:

• chr21-44935795-A-C
• chr21-44935795-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000330551.3(LINC01547):​n.493T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000629 in 317,852 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000063 (0 hom.)
• Consequence: LINC01547 ENST00000330551.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562
• Publications: 0 publications found

Genes affected

LINC01547 (HGNC:15707): (long intergenic non-protein coding RNA 1547) Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01547	NR_027128.1	n.417T>G		non_coding_transcript_exon_variant	Exon 2 of 4
LINC01547	NR_027129.1	n.561T>G		non_coding_transcript_exon_variant	Exon 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01547	ENST00000330551.3	n.493T>G		non_coding_transcript_exon_variant	Exon 3 of 4	1
LINC01547	ENST00000615847.3	n.1426T>G		non_coding_transcript_exon_variant	Exon 2 of 4	1
LINC01547	ENST00000397841.5	n.417T>G		non_coding_transcript_exon_variant	Exon 2 of 4	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000629 AC: 2 AN: 317852 Hom.: 0 Cov.: 0 AF XY: 0.0000111 AC XY: 2 AN XY: 179548

African (AFR) AF: 0.00 AC: 0 AN: 8392

American (AMR) AF: 0.00 AC: 0 AN: 27010

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10746

East Asian (EAS) AF: 0.00 AC: 0 AN: 9088

South Asian (SAS) AF: 0.0000336 AC: 2 AN: 59558

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28052

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2768

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 158006

Other (OTH) AF: 0.00 AC: 0 AN: 14232

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.33
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs11088971; hg19: chr21-46355710;