rs10495717

Positions:

• chr2-21702195-T-C

Variant summary

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

The NR_038837.1(LINC01822):​n.236+7954A>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 0.205 in 151,644 control chromosomes in the GnomAD database, including 5,881 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 0.20 (5881 hom., cov: 31)
• Consequence: LINC01822 NR_038837.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

Genes affected

(HGNC:):

LINC01822 (HGNC:52627): (long intergenic non-protein coding RNA 1822)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01822	NR_038837.1	n.236+7954A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435237.1	n.194-97162T>C		intron_variant, non_coding_transcript_variant		3
LINC01822	ENST00000668104.1	n.240+7954A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30986 AN: 151526 Hom.: 5856 Cov.: 31

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0514

Gnomad SAS AF: 0.0450

Gnomad FIN AF: 0.0425

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0904

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.205 AC: 31053 AN: 151644 Hom.: 5881 Cov.: 31 AF XY: 0.198 AC XY: 14675 AN XY: 74132

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.0509

Gnomad4 SAS AF: 0.0448

Gnomad4 FIN AF: 0.0425

Gnomad4 NFE AF: 0.0904

Gnomad4 OTH AF: 0.180

Alfa AF: 0.114 Hom.: 948

Bravo AF: 0.228

Asia WGS AF: 0.0870 AC: 302 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.25
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495717; hg19: chr2-21925067;