chr9-90647075-A-G

Variant names:

• chr9-90647075-A-G
• rs1831521

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 0.682 in 152,054 control chromosomes in the GnomAD database, including 35,910 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 0.68 (35910 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.771 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: 0.682 AC: 103587 AN: 151936 Hom.: 35894 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.818

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.682 AC: 103655 AN: 152054 Hom.: 35910 Cov.: 32 AF XY: 0.679 AC XY: 50506 AN XY: 74330

African (AFR) AF: 0.595 AC: 24668 AN: 41440

American (AMR) AF: 0.626 AC: 9571 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2738 AN: 3472

East Asian (EAS) AF: 0.442 AC: 2280 AN: 5156

South Asian (SAS) AF: 0.792 AC: 3825 AN: 4830

European-Finnish (FIN) AF: 0.672 AC: 7106 AN: 10570

Middle Eastern (MID) AF: 0.805 AC: 235 AN: 292

European-Non Finnish (NFE) AF: 0.751 AC: 51028 AN: 67988

Other (OTH) AF: 0.730 AC: 1541 AN: 2112

Alfa AF: 0.720 Hom.: 97127

Bravo AF: 0.671

Asia WGS AF: 0.618 AC: 2149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.081
DANN	Benign	0.38
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1831521; hg19: chr9-93409357;