rs9574536

Variant names:

• chr13-80010956-T-C
• rs9574536
• ENST00000648514.1:n.827+36078A>G

Variant summary

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

The ENST00000648514.1(ENSG00000284196):​n.827+36078A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,126 control chromosomes in the GnomAD database, including 18,789 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 0.47 (18788 hom., cov: 32)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: ENSG00000284196 ENST00000648514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56
• Publications: 3 publications found

Genes affected

ENSG00000284196 (HGNC:):

LINC01080 (HGNC:49123): (long intergenic non-protein coding RNA 1080)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648514.1. 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
	LINC01080	NR_104138.1		n.-121T>C		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000284196	ENST00000648514.1		n.827+36078A>G		intron	N/A
	LINC01080	ENST00000627044.1	TSL:4	n.-121T>C		upstream_gene	N/A
	LINC01080	ENST00000776551.1		n.-157T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71670 AN: 152004 Hom.: 18792 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.531

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 AC XY: 0 AN XY: 0

⚠️ 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: 1.00 AC: 2 AN: 2

Other (OTH) AF: 0.500 AC: 1 AN: 2

⚠️ 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: 0.471 AC: 71682 AN: 152122 Hom.: 18788 Cov.: 32 AF XY: 0.467 AC XY: 34728 AN XY: 74366

African (AFR) AF: 0.239 AC: 9932 AN: 41520

American (AMR) AF: 0.591 AC: 9025 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1793 AN: 3462

East Asian (EAS) AF: 0.406 AC: 2095 AN: 5166

South Asian (SAS) AF: 0.381 AC: 1836 AN: 4818

European-Finnish (FIN) AF: 0.480 AC: 5082 AN: 10592

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40149 AN: 67984

Other (OTH) AF: 0.525 AC: 1107 AN: 2110

Alfa AF: 0.555 Hom.: 34704

Bravo AF: 0.475

Asia WGS AF: 0.356 AC: 1237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	7.8
DANN	Benign	0.77
PhyloP100		1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9574536;

hg19: chr13-80585091;