ENST00000453420.5:n.523+2212C>T

Variant names:

• chr21-28210028-G-A
• rs2831649
• ENST00000453420.5:n.523+2212C>T

Variant summary

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

The ENST00000453420.5(LINC01695):​n.523+2212C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,088 control chromosomes in the GnomAD database, including 5,015 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 (5015 hom., cov: 33)
• Consequence: LINC01695 ENST00000453420.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176
• Publications: 3 publications found

Genes affected

LINC01695 (HGNC:52483): (long intergenic non-protein coding RNA 1695)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453420.5. 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
	LINC01695	NR_126012.1		n.523+2212C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01695	ENST00000453420.5	TSL:1	n.523+2212C>T		intron	N/A
	LINC01695	ENST00000437194.2	TSL:3	n.531-43C>T		intron	N/A
	LINC01695	ENST00000662491.1		n.435-43C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37752 AN: 151970 Hom.: 4996 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.249 AC: 37813 AN: 152088 Hom.: 5015 Cov.: 33 AF XY: 0.246 AC XY: 18298 AN XY: 74346

African (AFR) AF: 0.266 AC: 11019 AN: 41478

American (AMR) AF: 0.268 AC: 4101 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 779 AN: 3470

East Asian (EAS) AF: 0.465 AC: 2389 AN: 5142

South Asian (SAS) AF: 0.131 AC: 633 AN: 4820

European-Finnish (FIN) AF: 0.215 AC: 2279 AN: 10584

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15913 AN: 67986

Other (OTH) AF: 0.262 AC: 553 AN: 2112

Alfa AF: 0.256 Hom.: 985

Bravo AF: 0.258

Asia WGS AF: 0.295 AC: 1025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.66
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs2831649; hg19: chr21-29582347;