21-36437079-A-G

Variant names:

• chr21-36437079-A-G
• rs9984974
• ENST00000428667.2:n.88+6667A>G

Variant summary

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

The ENST00000428667.2(LNCTSI):​n.88+6667A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,008 control chromosomes in the GnomAD database, including 7,968 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 0.28 (7968 hom., cov: 32)
• Consequence: LNCTSI ENST00000428667.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.898
• Publications: 5 publications found

Genes affected

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

CLDN14-AS1 (HGNC:55953): (CLDN14 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428667.2. 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
	CLDN14-AS1	NR_183529.1		n.88+6667A>G		intron	N/A
	CLDN14-AS1	NR_183530.1		n.88+6667A>G		intron	N/A
	CLDN14-AS1	NR_183531.1		n.88+6667A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNCTSI	ENST00000428667.2	TSL:5	n.88+6667A>G		intron	N/A
	LNCTSI	ENST00000429588.1	TSL:3	n.53+6667A>G		intron	N/A
	LNCTSI	ENST00000715798.1		n.88+6667A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42510 AN: 151890 Hom.: 7963 Cov.: 32

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.280 AC: 42546 AN: 152008 Hom.: 7968 Cov.: 32 AF XY: 0.281 AC XY: 20848 AN XY: 74292

African (AFR) AF: 0.515 AC: 21343 AN: 41414

American (AMR) AF: 0.230 AC: 3511 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3472

East Asian (EAS) AF: 0.425 AC: 2194 AN: 5168

South Asian (SAS) AF: 0.444 AC: 2132 AN: 4806

European-Finnish (FIN) AF: 0.149 AC: 1575 AN: 10570

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10271 AN: 68008

Other (OTH) AF: 0.252 AC: 533 AN: 2114

Alfa AF: 0.207 Hom.: 8197

Bravo AF: 0.296

Asia WGS AF: 0.469 AC: 1631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.1
DANN	Benign	0.67
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs9984974; hg19: chr21-37809377;