chr13-22179954-A-G

Variant names:

• chr13-22179954-A-G
• rs9580312
• ENST00000611481.1:n.165+72320A>G

Variant summary

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

The ENST00000611481.1(LINC00540):​n.165+72320A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,102 control chromosomes in the GnomAD database, including 2,537 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 0.17 (2537 hom., cov: 31)
• Consequence: LINC00540 ENST00000611481.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780
• Publications: 3 publications found

Genes affected

LINC00540 (HGNC:43673): (long intergenic non-protein coding RNA 540)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000611481.1. 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
	LINC00540	ENST00000611481.1	TSL:4	n.165+72320A>G		intron	N/A
	LINC00540	ENST00000631321.1	TSL:2	n.411-94569A>G		intron	N/A
	LINC00540	ENST00000657205.1		n.414-3979A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25666 AN: 151984 Hom.: 2537 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.169 AC: 25676 AN: 152102 Hom.: 2537 Cov.: 31 AF XY: 0.176 AC XY: 13075 AN XY: 74346

African (AFR) AF: 0.108 AC: 4501 AN: 41508

American (AMR) AF: 0.239 AC: 3644 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 439 AN: 3472

East Asian (EAS) AF: 0.402 AC: 2079 AN: 5166

South Asian (SAS) AF: 0.323 AC: 1560 AN: 4824

European-Finnish (FIN) AF: 0.184 AC: 1945 AN: 10586

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11014 AN: 67960

Other (OTH) AF: 0.171 AC: 361 AN: 2110

Alfa AF: 0.165 Hom.: 4470

Bravo AF: 0.171

Asia WGS AF: 0.335 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.72
DANN	Benign	0.71
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs9580312; hg19: chr13-22754093;