rs894520

Variant names:

• chr9-38189530-T-C
• rs894520
• ENST00000788307.1:n.89-6107A>G

Variant summary

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

The ENST00000788307.1(ENSG00000302636):​n.89-6107A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,988 control chromosomes in the GnomAD database, including 10,417 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 0.36 (10417 hom., cov: 32)
• Consequence: ENSG00000302636 ENST00000788307.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 9 publications found

Genes affected

ENSG00000302636 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000788307.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302636	ENST00000788307.1		n.89-6107A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55355 AN: 151870 Hom.: 10404 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.365 AC: 55405 AN: 151988 Hom.: 10417 Cov.: 32 AF XY: 0.361 AC XY: 26783 AN XY: 74280

African (AFR) AF: 0.473 AC: 19574 AN: 41418

American (AMR) AF: 0.344 AC: 5260 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 913 AN: 3468

East Asian (EAS) AF: 0.296 AC: 1533 AN: 5172

South Asian (SAS) AF: 0.400 AC: 1929 AN: 4820

European-Finnish (FIN) AF: 0.282 AC: 2974 AN: 10560

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.326 AC: 22134 AN: 67958

Other (OTH) AF: 0.351 AC: 740 AN: 2110

Alfa AF: 0.336 Hom.: 26080

Bravo AF: 0.370

Asia WGS AF: 0.359 AC: 1248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.69
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs894520; hg19: chr9-38189527;