rs2831605

Positions:

• chr21-28172874-C-T

Variant summary

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

The NR_126012.1(LINC01695):​n.524-2731G>A 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 0.124 in 151,660 control chromosomes in the GnomAD database, including 1,222 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 0.12 (1222 hom., cov: 31)
• Consequence: LINC01695 NR_126012.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.823

Genes affected

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01695	NR_126012.1	n.524-2731G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01695	ENST00000453420.5	n.524-2731G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18776 AN: 151546 Hom.: 1217 Cov.: 31

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.00620

Gnomad SAS AF: 0.0547

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.124 AC: 18794 AN: 151660 Hom.: 1222 Cov.: 31 AF XY: 0.123 AC XY: 9125 AN XY: 74096

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.00622

Gnomad4 SAS AF: 0.0549

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.130

Alfa AF: 0.132 Hom.: 224

Bravo AF: 0.122

Asia WGS AF: 0.0450 AC: 160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2831605; hg19: chr21-29545193;