9-110821732-A-G

Variant names:

• chr9-110821732-A-G
• rs2767001

Variant summary

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

The variant allele was found at a frequency of 0.738 in 152,066 control chromosomes in the GnomAD database, including 41,749 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 (41749 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119
• Publications: 5 publications found

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 (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112172 AN: 151948 Hom.: 41704 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.738 AC: 112278 AN: 152066 Hom.: 41749 Cov.: 31 AF XY: 0.747 AC XY: 55492 AN XY: 74334

African (AFR) AF: 0.691 AC: 28657 AN: 41456

American (AMR) AF: 0.787 AC: 12026 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2628 AN: 3466

East Asian (EAS) AF: 0.955 AC: 4932 AN: 5162

South Asian (SAS) AF: 0.841 AC: 4057 AN: 4826

European-Finnish (FIN) AF: 0.810 AC: 8583 AN: 10590

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49147 AN: 67962

Other (OTH) AF: 0.728 AC: 1538 AN: 2114

Alfa AF: 0.732 Hom.: 69996

Bravo AF: 0.732

Asia WGS AF: 0.895 AC: 3110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.25
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2767001; hg19: chr9-113584012;