rs12337364

Positions:

• chr9-21430132-C-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 0.0972 in 152,154 control chromosomes in the GnomAD database, including 750 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 0.097 (750 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.21430132C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000698343.1	n.103-9440G>A		intron_variant
MIR31HG	ENST00000698344.1	n.497-9440G>A		intron_variant
MIR31HG	ENST00000698345.1	n.255-9440G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0972 AC: 14777 AN: 152036 Hom.: 746 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0971

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.0876

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

GnomAD4 genome AF: 0.0972 AC: 14782 AN: 152154 Hom.: 750 Cov.: 32 AF XY: 0.0987 AC XY: 7341 AN XY: 74382

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0741

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.0968

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0803

Gnomad4 OTH AF: 0.0863

Alfa AF: 0.0556 Hom.: 72

Bravo AF: 0.0984

Asia WGS AF: 0.132 AC: 459 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12337364; hg19: chr9-21430131;