chr21-28124014-A-G

Position:

• chr21-28124014-A-G

Variant summary

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

The NR_126010.1(LINC01697):​n.345-6516A>G 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 0.143 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: LINC01697 NR_126010.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.05

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC01697	NR_126010.1	n.345-6516A>G		intron_variant, non_coding_transcript_variant
LINC01695	NR_126012.1	n.706-4140T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01697	ENST00000426534.2	n.355-6516A>G		intron_variant, non_coding_transcript_variant		2
LINC01695	ENST00000453420.5	n.706-4140T>C		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.0949

Gnomad4 EAS AF: 0.0941

Gnomad4 SAS AF: 0.0491

Gnomad4 FIN AF: 0.0367

Gnomad4 NFE AF: 0.0684

Gnomad4 OTH AF: 0.139

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9981984; hg19: chr21-29496333;