ENST00000453420.5:n.706-4140T>C

Variant names:

• chr21-28124014-A-G
• rs9981984
• ENST00000453420.5:n.706-4140T>C

Variant summary

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

The ENST00000453420.5(LINC01695):​n.706-4140T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,180 control chromosomes in the GnomAD database, including 2,269 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 0.14 (2269 hom., cov: 33)
• Consequence: LINC01695 ENST00000453420.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.05
• Publications: 1 publications found

Genes affected

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

LINC01697 (HGNC:52485): (long intergenic non-protein coding RNA 1697)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01697	NR_126010.1	n.345-6516A>G		intron_variant	Intron 2 of 4
LINC01695	NR_126012.1	n.706-4140T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01695	ENST00000453420.5	n.706-4140T>C		intron_variant	Intron 5 of 5	1
LINC01697	ENST00000426534.2	n.355-6516A>G		intron_variant	Intron 2 of 4	2
LINC01695	ENST00000737222.1	n.192-160T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21698 AN: 152062 Hom.: 2270 Cov.: 33

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.0949

Gnomad EAS AF: 0.0942

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.0367

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0684

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.143 AC: 21721 AN: 152180 Hom.: 2269 Cov.: 33 AF XY: 0.142 AC XY: 10557 AN XY: 74404

African (AFR) AF: 0.285 AC: 11835 AN: 41490

American (AMR) AF: 0.222 AC: 3385 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0949 AC: 328 AN: 3458

East Asian (EAS) AF: 0.0941 AC: 488 AN: 5188

South Asian (SAS) AF: 0.0491 AC: 237 AN: 4824

European-Finnish (FIN) AF: 0.0367 AC: 390 AN: 10616

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0684 AC: 4651 AN: 68004

Other (OTH) AF: 0.139 AC: 295 AN: 2116

Alfa AF: 0.112 Hom.: 201

Bravo AF: 0.165

Asia WGS AF: 0.112 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.3
DANN	Benign	0.59
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs9981984; hg19: chr21-29496333;