chr9-11951222-C-A

Variant names:

• chr9-11951222-C-A
• rs1929412
• ENST00000649122.1:n.388+23283C>A

Variant summary

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

The ENST00000649122.1(ENSG00000285784):​n.388+23283C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0689 in 151,706 control chromosomes in the GnomAD database, including 695 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 0.069 (695 hom., cov: 32)
• Consequence: ENSG00000285784 ENST00000649122.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747
• Publications: 3 publications found

Genes affected

ENSG00000285784 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649122.1. 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
	ENSG00000285784	ENST00000649122.1		n.388+23283C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0687 AC: 10417 AN: 151588 Hom.: 691 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.0274

Gnomad FIN AF: 0.0344

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0268

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0689 AC: 10446 AN: 151706 Hom.: 695 Cov.: 32 AF XY: 0.0691 AC XY: 5123 AN XY: 74166

African (AFR) AF: 0.130 AC: 5354 AN: 41192

American (AMR) AF: 0.113 AC: 1722 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0228 AC: 79 AN: 3470

East Asian (EAS) AF: 0.161 AC: 827 AN: 5134

South Asian (SAS) AF: 0.0272 AC: 131 AN: 4818

European-Finnish (FIN) AF: 0.0344 AC: 364 AN: 10596

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.0268 AC: 1819 AN: 67948

Other (OTH) AF: 0.0625 AC: 132 AN: 2112

Alfa AF: 0.0389 Hom.: 426

Bravo AF: 0.0770

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.63
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs1929412; hg19: chr9-11951222;