chr21-28137610-A-C

Position:

• chr21-28137610-A-C

Variant summary

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

The ENST00000426534.2(LINC01697):​n.1763A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,950 control chromosomes in the GnomAD database, including 22,787 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 0.54 (22787 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01697 ENST00000426534.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.40

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01695	NR_126012.1	n.706-17736T>G		intron_variant, non_coding_transcript_variant
LINC01697	NR_126010.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01697	ENST00000426534.2	n.1763A>C		non_coding_transcript_exon_variant	5/5	2
LINC01695	ENST00000453420.5	n.706-17736T>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81943 AN: 151832 Hom.: 22739 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.508

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.540 AC: 82051 AN: 151950 Hom.: 22787 Cov.: 32 AF XY: 0.536 AC XY: 39784 AN XY: 74244

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.513

Alfa AF: 0.537 Hom.: 3518

Bravo AF: 0.554

Asia WGS AF: 0.448 AC: 1550 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1571671; hg19: chr21-29509929;