21-28103172-G-T

Variant names:

• chr21-28103172-G-T
• rs2831489
• ENST00000458316.2:n.723G>T

Variant summary

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

The ENST00000458316.2(LINC01697):​n.723G>T 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 0.0869 in 152,092 control chromosomes in the GnomAD database, including 660 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 0.087 (660 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01697 ENST00000458316.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.947
• Publications: 0 publications found

Genes affected

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01697	NR_126011.1	n.796G>T		non_coding_transcript_exon_variant	Exon 3 of 3
LINC01697	NR_126010.1	n.344+403G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01697	ENST00000458316.2	n.723G>T		non_coding_transcript_exon_variant	Exon 2 of 2	1
LINC01697	ENST00000436878.2	n.960G>T		non_coding_transcript_exon_variant	Exon 3 of 3	2
LINC01697	ENST00000657256.1	n.832G>T		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0869 AC: 13211 AN: 151974 Hom.: 657 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0551

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.0351

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0834

Gnomad OTH AF: 0.0715

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0869 AC: 13221 AN: 152092 Hom.: 660 Cov.: 32 AF XY: 0.0855 AC XY: 6353 AN XY: 74314

African (AFR) AF: 0.121 AC: 5004 AN: 41480

American (AMR) AF: 0.0550 AC: 840 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0412 AC: 143 AN: 3468

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5180

South Asian (SAS) AF: 0.0351 AC: 169 AN: 4810

European-Finnish (FIN) AF: 0.109 AC: 1155 AN: 10572

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0833 AC: 5666 AN: 67990

Other (OTH) AF: 0.0708 AC: 149 AN: 2106

Alfa AF: 0.0912 Hom.: 97

Bravo AF: 0.0846

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.53
DANN	Benign	0.65
PhyloP100		-0.95
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2831489; hg19: chr21-29475491;