9-129565357-T-C

Variant names:

• chr9-129565357-T-C
• rs1220646
• ENST00000804796.1:n.473+1284A>G

Variant summary

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

The ENST00000804796.1(ENSG00000304586):​n.473+1284A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 151,836 control chromosomes in the GnomAD database, including 41,884 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 0.74 (41884 hom., cov: 30)
• Consequence: ENSG00000304586 ENST00000804796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.23
• Publications: 0 publications found

Genes affected

ENSG00000304586 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804796.1. 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
	ENSG00000304586	ENST00000804796.1		n.473+1284A>G		intron	N/A
	ENSG00000304586	ENST00000804797.1		n.191-2741A>G		intron	N/A
	ENSG00000304586	ENST00000804798.1		n.182-2741A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112335 AN: 151722 Hom.: 41846 Cov.: 30

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.740 AC: 112427 AN: 151836 Hom.: 41884 Cov.: 30 AF XY: 0.741 AC XY: 54971 AN XY: 74218

African (AFR) AF: 0.656 AC: 27137 AN: 41336

American (AMR) AF: 0.784 AC: 11963 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2614 AN: 3468

East Asian (EAS) AF: 0.750 AC: 3829 AN: 5108

South Asian (SAS) AF: 0.692 AC: 3323 AN: 4800

European-Finnish (FIN) AF: 0.772 AC: 8160 AN: 10574

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.780 AC: 53012 AN: 67972

Other (OTH) AF: 0.743 AC: 1567 AN: 2108

Alfa AF: 0.758 Hom.: 5450

Bravo AF: 0.738

Asia WGS AF: 0.699 AC: 2433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.51
DANN	Benign	0.48
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs1220646; hg19: chr9-132327636;