rs9612574

Variant names:

• chr22-20656929-G-C
• rs9612574
• ENST00000443839.1:n.-15C>G

Variant summary

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

The ENST00000443839.1(ENSG00000290981):​n.-15C>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0853 in 152,302 control chromosomes in the GnomAD database, including 599 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 0.085 (598 hom., cov: 31)
  • Exomes 𝑓: 0.16 (1 hom.)
• Consequence: ENSG00000290981 ENST00000443839.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201

Genes affected

ENSG00000290981 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290981	ENST00000443839.1	n.-15C>G		upstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.0853 AC: 12968 AN: 152110 Hom.: 598 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.0722

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.0485

Gnomad SAS AF: 0.0665

Gnomad FIN AF: 0.0567

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0727

Gnomad OTH AF: 0.0938

GnomAD4 exome AF: 0.162 AC: 12 AN: 74 Hom.: 1 Cov.: 0 AF XY: 0.115 AC XY: 6 AN XY: 52

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.0853 AC: 12983 AN: 152228 Hom.: 598 Cov.: 31 AF XY: 0.0839 AC XY: 6244 AN XY: 74426

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.0721

Gnomad4 ASJ AF: 0.0772

Gnomad4 EAS AF: 0.0483

Gnomad4 SAS AF: 0.0673

Gnomad4 FIN AF: 0.0567

Gnomad4 NFE AF: 0.0727

Gnomad4 OTH AF: 0.0933

Alfa AF: 0.0736 Hom.: 45

Bravo AF: 0.0884

Asia WGS AF: 0.0620 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	1.6
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9612574; hg19: chr22-21011216;