21-28540130-C-A

Variant names:

• chr21-28540130-C-A
• rs2150392
• ENST00000412526.5:n.645C>A

Variant summary

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

The ENST00000412526.5(LINC00161):​n.645C>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 0.501 in 151,922 control chromosomes in the GnomAD database, including 22,528 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 0.50 (22526 hom., cov: 31)
  • Exomes 𝑓: 0.83 (2 hom.)
• Consequence: LINC00161 ENST00000412526.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.850
• Publications: 7 publications found

Genes affected

LINC00161 (HGNC:17138): (long intergenic non-protein coding RNA 161)

LINC03138 (HGNC:58104):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412526.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00161	NR_026552.2		n.645C>A		non_coding_transcript_exon	Exon 2 of 2
	LINC00161	NR_026553.2		n.289C>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00161	ENST00000412526.5	TSL:2	n.645C>A		non_coding_transcript_exon	Exon 2 of 2
	LINC00161	ENST00000455939.1	TSL:2	n.289C>A		non_coding_transcript_exon	Exon 2 of 2
	LINC00161	ENST00000825125.1		n.340C>A		non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76133 AN: 151798 Hom.: 22530 Cov.: 31

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.543

GnomAD4 exome AF: 0.833 AC: 5 AN: 6 Hom.: 2 Cov.: 0 AF XY: 0.833 AC XY: 5 AN XY: 6

⚠️ 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: 0.833 AC: 5 AN: 6

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.501 AC: 76129 AN: 151916 Hom.: 22526 Cov.: 31 AF XY: 0.502 AC XY: 37282 AN XY: 74246

African (AFR) AF: 0.208 AC: 8617 AN: 41424

American (AMR) AF: 0.486 AC: 7414 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2048 AN: 3468

East Asian (EAS) AF: 0.182 AC: 940 AN: 5154

South Asian (SAS) AF: 0.476 AC: 2290 AN: 4808

European-Finnish (FIN) AF: 0.734 AC: 7740 AN: 10546

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45185 AN: 67964

Other (OTH) AF: 0.538 AC: 1129 AN: 2100

Alfa AF: 0.598 Hom.: 14729

Bravo AF: 0.469

Asia WGS AF: 0.280 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.67
DANN	Benign	0.82
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs2150392; hg19: chr21-29912452;