21-36441816-T-C

Variant names:

• chr21-36441816-T-C
• rs2835349
• ENST00000428667.2:n.89-3812T>C

Variant summary

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

The ENST00000428667.2(LNCTSI):​n.89-3812T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 152,014 control chromosomes in the GnomAD database, including 25,900 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 0.58 (25900 hom., cov: 32)
• Consequence: LNCTSI ENST00000428667.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512
• Publications: 9 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.658 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.89-3812T>C		intron	N/A
	CLDN14-AS1	NR_183530.1		n.89-3812T>C		intron	N/A
	CLDN14-AS1	NR_183531.1		n.89-3812T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNCTSI	ENST00000428667.2	TSL:5	n.89-3812T>C		intron	N/A
	LNCTSI	ENST00000429588.1	TSL:3	n.53+11404T>C		intron	N/A
	LNCTSI	ENST00000715798.1		n.89-3812T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88206 AN: 151896 Hom.: 25902 Cov.: 32

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.580 AC: 88237 AN: 152014 Hom.: 25900 Cov.: 32 AF XY: 0.581 AC XY: 43195 AN XY: 74318

African (AFR) AF: 0.657 AC: 27232 AN: 41476

American (AMR) AF: 0.549 AC: 8375 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1798 AN: 3466

East Asian (EAS) AF: 0.506 AC: 2613 AN: 5168

South Asian (SAS) AF: 0.677 AC: 3265 AN: 4820

European-Finnish (FIN) AF: 0.557 AC: 5890 AN: 10568

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37225 AN: 67954

Other (OTH) AF: 0.539 AC: 1132 AN: 2100

Alfa AF: 0.539 Hom.: 16924

Bravo AF: 0.579

Asia WGS AF: 0.607 AC: 2114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.49
DANN	Benign	0.54
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs2835349; hg19: chr21-37814114;