chr2-10848462-C-A

Variant names:

• chr2-10848462-C-A
• rs9287724
• ENST00000744008.1:n.2G>T

Variant summary

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

The ENST00000744008.1(ENSG00000296979):​n.2G>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 0.161 in 152,196 control chromosomes in the GnomAD database, including 2,223 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 0.16 (2223 hom., cov: 32)
• Consequence: ENSG00000296979 ENST00000744008.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 8 publications found

Genes affected

ENSG00000296979 (HGNC:):

LINC01954 (HGNC:52779): (long intergenic non-protein coding RNA 1954)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000744008.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296979	ENST00000744008.1		n.2G>T		non_coding_transcript_exon	Exon 1 of 2
	LINC01954	ENST00000418835.1	TSL:3	n.35+851C>A		intron	N/A
	LINC01954	ENST00000670239.2		n.272+3957C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24429 AN: 152078 Hom.: 2218 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0580

Gnomad EAS AF: 0.0321

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.161 AC: 24453 AN: 152196 Hom.: 2223 Cov.: 32 AF XY: 0.163 AC XY: 12117 AN XY: 74398

African (AFR) AF: 0.173 AC: 7171 AN: 41536

American (AMR) AF: 0.125 AC: 1915 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0580 AC: 201 AN: 3468

East Asian (EAS) AF: 0.0322 AC: 167 AN: 5184

South Asian (SAS) AF: 0.137 AC: 661 AN: 4824

European-Finnish (FIN) AF: 0.265 AC: 2800 AN: 10578

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11015 AN: 67988

Other (OTH) AF: 0.143 AC: 303 AN: 2114

Alfa AF: 0.150 Hom.: 7862

Bravo AF: 0.148

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.35
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9287724; hg19: chr2-10988588;