21-36580889-A-G

Variant names:

• chr21-36580889-A-G
• rs432137
• ENST00000660763.1:n.477A>G

Variant summary

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

The ENST00000660763.1(ENSG00000286852):​n.477A>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 0.537 in 151,974 control chromosomes in the GnomAD database, including 22,630 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 0.54 (22630 hom., cov: 32)
• Consequence: ENSG00000286852 ENST00000660763.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986
• Publications: 3 publications found

Genes affected

ENSG00000286852 (HGNC:):

LNCTSI (HGNC:56660): (lncRNA TGF-beta/SMAD3 pathway interacting)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286852	ENST00000660763.1	n.477A>G		non_coding_transcript_exon_variant	Exon 2 of 2
LNCTSI	ENST00000715798.1	n.469-46106A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81548 AN: 151856 Hom.: 22622 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.537 AC: 81596 AN: 151974 Hom.: 22630 Cov.: 32 AF XY: 0.534 AC XY: 39668 AN XY: 74292

African (AFR) AF: 0.385 AC: 15973 AN: 41454

American (AMR) AF: 0.538 AC: 8220 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2107 AN: 3472

East Asian (EAS) AF: 0.578 AC: 2980 AN: 5158

South Asian (SAS) AF: 0.539 AC: 2595 AN: 4814

European-Finnish (FIN) AF: 0.570 AC: 6013 AN: 10558

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.615 AC: 41770 AN: 67928

Other (OTH) AF: 0.555 AC: 1171 AN: 2110

Alfa AF: 0.589 Hom.: 83116

Bravo AF: 0.528

Asia WGS AF: 0.527 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.59
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs432137; hg19: chr21-37953187;