rs9580312

Positions:

• chr13-22179954-A-G
• chr13-22179954-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22179954A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00540	ENST00000611481.1	n.165+72320A>G		intron_variant		4
LINC00540	ENST00000631321.1	n.411-94569A>G		intron_variant		2
LINC00540	ENST00000657205.1	n.414-3979A>G		intron_variant

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

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.171

Alfa AF: 0.162 Hom.: 3163

Bravo AF: 0.171

Asia WGS AF: 0.335 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9580312; hg19: chr13-22754093;