rs219781

Positions:

• chr21-36460323-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_183529.1(CLDN14-AS1):​n.468+14316G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,130 control chromosomes in the GnomAD database, including 4,905 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 0.25 (4902 hom., cov: 32)
  • Exomes 𝑓: 0.19 (3 hom.)
• Consequence: CLDN14-AS1 NR_183529.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLDN14-AS1	NR_183529.1	n.468+14316G>T		intron_variant, non_coding_transcript_variant
CLDN14-AS1	NR_183532.1	n.502G>T		non_coding_transcript_exon_variant	3/3
CLDN14-AS1	NR_183530.1	n.468+14316G>T		intron_variant, non_coding_transcript_variant
CLDN14-AS1	NR_183531.1	n.468+14316G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLDN14-AS1	ENST00000428667.1	n.277+14316G>T		intron_variant, non_coding_transcript_variant		5
LNCTSI	ENST00000429588.1	n.54-19908G>T		intron_variant, non_coding_transcript_variant		3
CLDN14-AS1	ENST00000454980.1	n.220G>T		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37420 AN: 151976 Hom.: 4883 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.00751

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.260

GnomAD4 exome AF: 0.194 AC: 7 AN: 36 Hom.: 3 Cov.: 0 AF XY: 0.0625 AC XY: 1 AN XY: 16

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.233

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.246 AC: 37487 AN: 152094 Hom.: 4902 Cov.: 32 AF XY: 0.240 AC XY: 17829 AN XY: 74370

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.00753

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.258

Alfa AF: 0.250 Hom.: 6521

Bravo AF: 0.248

Asia WGS AF: 0.109 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs219781; hg19: chr21-37832621;