10-121185572-A-G

Variant names:

• chr10-121185572-A-G
• rs3943077
• ENST00000429809.1:n.2470A>G

Variant summary

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

The ENST00000429809.1(LINC01153):​n.2470A>G 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 0.593 in 151,900 control chromosomes in the GnomAD database, including 29,558 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 0.59 (29549 hom., cov: 30)
  • Exomes 𝑓: 0.88 (9 hom.)
• Consequence: LINC01153 ENST00000429809.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.577
• Publications: 10 publications found

Genes affected

LINC01153 (HGNC:49495): (long intergenic non-protein coding RNA 1153)

ENSG00000296663 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429809.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01153	ENST00000429809.1	TSL:1	n.2470A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000296663	ENST00000741064.1		n.-102T>C		upstream_gene	N/A
	ENSG00000296663	ENST00000741065.1		n.-102T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90065 AN: 151758 Hom.: 29557 Cov.: 30

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.637

GnomAD4 exome AF: 0.875 AC: 21 AN: 24 Hom.: 9 Cov.: 0 AF XY: 0.786 AC XY: 11 AN XY: 14

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

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: 0.875 AC: 21 AN: 24

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0186682), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.593 AC: 90075 AN: 151876 Hom.: 29549 Cov.: 30 AF XY: 0.591 AC XY: 43839 AN XY: 74234

African (AFR) AF: 0.313 AC: 12963 AN: 41394

American (AMR) AF: 0.555 AC: 8470 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2949 AN: 3468

East Asian (EAS) AF: 0.397 AC: 2039 AN: 5130

South Asian (SAS) AF: 0.801 AC: 3847 AN: 4804

European-Finnish (FIN) AF: 0.698 AC: 7383 AN: 10576

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.736 AC: 50026 AN: 67930

Other (OTH) AF: 0.636 AC: 1339 AN: 2104

Alfa AF: 0.668 Hom.: 54124

Bravo AF: 0.564

Asia WGS AF: 0.576 AC: 2005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.77
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs3943077; hg19: chr10-122945086;