9-82852892-A-G

Variant names:

• chr9-82852892-A-G
• rs10121793
• ENST00000792604.1:n.266-21766T>C

Variant summary

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

The ENST00000792604.1(ENSG00000303186):​n.266-21766T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0805 in 152,156 control chromosomes in the GnomAD database, including 1,526 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 0.081 (1526 hom., cov: 32)
• Consequence: ENSG00000303186 ENST00000792604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 1 publications found

Genes affected

ENSG00000303186 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792604.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303186	ENST00000792604.1		n.266-21766T>C		intron	N/A
	ENSG00000303186	ENST00000792605.1		n.113-21766T>C		intron	N/A
	ENSG00000303186	ENST00000792606.1		n.75-21766T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0804 AC: 12225 AN: 152038 Hom.: 1522 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0390

Gnomad ASJ AF: 0.00923

Gnomad EAS AF: 0.0422

Gnomad SAS AF: 0.00994

Gnomad FIN AF: 0.00999

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00243

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0805 AC: 12253 AN: 152156 Hom.: 1526 Cov.: 32 AF XY: 0.0781 AC XY: 5809 AN XY: 74412

African (AFR) AF: 0.264 AC: 10969 AN: 41482

American (AMR) AF: 0.0390 AC: 595 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.00923 AC: 32 AN: 3466

East Asian (EAS) AF: 0.0417 AC: 216 AN: 5180

South Asian (SAS) AF: 0.00974 AC: 47 AN: 4824

European-Finnish (FIN) AF: 0.00999 AC: 106 AN: 10610

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00243 AC: 165 AN: 68012

Other (OTH) AF: 0.0539 AC: 114 AN: 2114

Alfa AF: 0.0218 Hom.: 82

Bravo AF: 0.0930

Asia WGS AF: 0.0460 AC: 162 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.78
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10121793; hg19: chr9-85467807;