9-79807917-A-G

Variant names:

• chr9-79807917-A-G
• rs10512091
• ENST00000809831.1:n.104-4571A>G

Variant summary

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

The ENST00000809831.1(ENSG00000305253):​n.104-4571A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 152,074 control chromosomes in the GnomAD database, including 49,370 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 0.80 (49370 hom., cov: 30)
• Consequence: ENSG00000305253 ENST00000809831.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 5 publications found

Genes affected

ENSG00000305253 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809831.1. 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
	ENSG00000305253	ENST00000809831.1		n.104-4571A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.803 AC: 121968 AN: 151956 Hom.: 49337 Cov.: 30

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.803 AC: 122049 AN: 152074 Hom.: 49370 Cov.: 30 AF XY: 0.799 AC XY: 59385 AN XY: 74350

African (AFR) AF: 0.881 AC: 36561 AN: 41492

American (AMR) AF: 0.742 AC: 11341 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2828 AN: 3472

East Asian (EAS) AF: 0.696 AC: 3577 AN: 5142

South Asian (SAS) AF: 0.717 AC: 3451 AN: 4812

European-Finnish (FIN) AF: 0.762 AC: 8072 AN: 10588

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53669 AN: 67968

Other (OTH) AF: 0.800 AC: 1692 AN: 2114

Alfa AF: 0.790 Hom.: 26528

Bravo AF: 0.802

Asia WGS AF: 0.716 AC: 2491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.1
DANN	Benign	0.61
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs10512091; hg19: chr9-82422832; COSMIC: COSV60364153;