chr21-44935616-A-G

Variant names:

• chr21-44935616-A-G
• rs11088970
• ENST00000330551.3:n.661+11T>C

Variant summary

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

The ENST00000330551.3(LINC01547):​n.661+11T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 315,812 control chromosomes in the GnomAD database, including 30,400 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 0.49 (21741 hom., cov: 33)
  • Exomes 𝑓: 0.31 (8659 hom.)
• Consequence: LINC01547 ENST00000330551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.18
• Publications: 7 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000330551.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01547	NR_027128.1		n.585+11T>C		intron	N/A
	LINC01547	NR_027129.1		n.729+11T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01547	ENST00000330551.3	TSL:1	n.661+11T>C		intron	N/A
	LINC01547	ENST00000615847.3	TSL:1	n.1594+11T>C		intron	N/A
	LINC01547	ENST00000397841.5	TSL:2	n.585+11T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73739 AN: 152002 Hom.: 21695 Cov.: 33

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.434

GnomAD2 exomes AF: 0.358 AC: 18423 AN: 51464 AF XY: 0.338

Gnomad AFR exome AF: 0.833

Gnomad AMR exome AF: 0.392

Gnomad ASJ exome AF: 0.318

Gnomad EAS exome AF: 0.231

Gnomad FIN exome AF: 0.352

Gnomad NFE exome AF: 0.324

Gnomad OTH exome AF: 0.312

GnomAD4 exome AF: 0.310 AC: 50736 AN: 163692 Hom.: 8659 Cov.: 0 AF XY: 0.296 AC XY: 27075 AN XY: 91590

African (AFR) AF: 0.787 AC: 1393 AN: 1770

American (AMR) AF: 0.397 AC: 2600 AN: 6552

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 945 AN: 2816

East Asian (EAS) AF: 0.234 AC: 802 AN: 3422

South Asian (SAS) AF: 0.213 AC: 7993 AN: 37608

European-Finnish (FIN) AF: 0.350 AC: 8360 AN: 23856

Middle Eastern (MID) AF: 0.311 AC: 649 AN: 2088

European-Non Finnish (NFE) AF: 0.327 AC: 25702 AN: 78598

Other (OTH) AF: 0.328 AC: 2292 AN: 6982

GnomAD4 genome AF: 0.485 AC: 73843 AN: 152120 Hom.: 21741 Cov.: 33 AF XY: 0.480 AC XY: 35684 AN XY: 74380

African (AFR) AF: 0.837 AC: 34773 AN: 41540

American (AMR) AF: 0.447 AC: 6826 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1288 AN: 3468

East Asian (EAS) AF: 0.267 AC: 1380 AN: 5160

South Asian (SAS) AF: 0.209 AC: 1009 AN: 4826

European-Finnish (FIN) AF: 0.351 AC: 3723 AN: 10592

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23488 AN: 67950

Other (OTH) AF: 0.430 AC: 904 AN: 2100

Alfa AF: 0.431 Hom.: 6734

Bravo AF: 0.513

Asia WGS AF: 0.283 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.10
DANN	Benign	0.26
PhyloP100		-3.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11088970; hg19: chr21-46355531; COSMIC: COSV52419679;