rs10861038

Variant names:

• chr12-103559279-C-A
• rs10861038
• ENST00000550185.5:n.2523C>A

Your query was ambiguous. Multiple possible variants found:

• chr12-103559279-C-A
• chr12-103559279-C-T

Variant summary

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

The ENST00000550185.5(LINC02401):​n.2523C>A 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 0.0851 in 120,636 control chromosomes in the GnomAD database, including 390 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 0.085 (390 hom., cov: 30)
  • Exomes 𝑓: 0.036 (0 hom.)
• Consequence: LINC02401 ENST00000550185.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37
• Publications: 4 publications found

Genes affected

LINC02401 (HGNC:53328): (long intergenic non-protein coding RNA 2401)

ENSG00000286197 (HGNC:):

C12orf42 (HGNC:24729): (chromosome 12 open reading frame 42)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000550185.5. 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
	LINC02401	NR_110103.1		n.2523C>A		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02401	ENST00000550185.5	TSL:1	n.2523C>A		non_coding_transcript_exon	Exon 5 of 5
	ENSG00000286197	ENST00000650784.1		n.204+4368G>T		intron	N/A
	LINC02401	ENST00000654623.1		n.845+1683C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0852 AC: 10262 AN: 120488 Hom.: 387 Cov.: 30

Gnomad AFR AF: 0.0726

Gnomad AMI AF: 0.0575

Gnomad AMR AF: 0.0939

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0713

Gnomad FIN AF: 0.0898

Gnomad MID AF: 0.103

Gnomad NFE AF: 0.0897

Gnomad OTH AF: 0.0939

GnomAD4 exome AF: 0.0357 AC: 1 AN: 28 Hom.: 0 Cov.: 0 AF XY: 0.0455 AC XY: 1 AN XY: 22

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) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.0455 AC: 1 AN: 22

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0851 AC: 10267 AN: 120608 Hom.: 390 Cov.: 30 AF XY: 0.0861 AC XY: 5066 AN XY: 58816

African (AFR) AF: 0.0727 AC: 2821 AN: 38828

American (AMR) AF: 0.0937 AC: 1075 AN: 11472

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 260 AN: 2998

East Asian (EAS) AF: 0.121 AC: 622 AN: 5154

South Asian (SAS) AF: 0.0711 AC: 287 AN: 4034

European-Finnish (FIN) AF: 0.0898 AC: 573 AN: 6380

Middle Eastern (MID) AF: 0.100 AC: 24 AN: 240

European-Non Finnish (NFE) AF: 0.0897 AC: 4406 AN: 49120

Other (OTH) AF: 0.0932 AC: 162 AN: 1738

Alfa AF: 0.0641 Hom.: 589

Bravo AF: 0.0690

Asia WGS AF: 0.0860 AC: 301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.9
DANN	Benign	0.83
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs10861038; hg19: chr12-103953057;