chr9-90681249-A-G

Variant names:

• chr9-90681249-A-G
• rs1173100

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 0.214 in 152,054 control chromosomes in the GnomAD database, including 3,977 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 0.21 (3977 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 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: 0.215 AC: 32594 AN: 151934 Hom.: 3981 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.214 AC: 32599 AN: 152054 Hom.: 3977 Cov.: 32 AF XY: 0.217 AC XY: 16124 AN XY: 74322

African (AFR) AF: 0.144 AC: 5981 AN: 41498

American (AMR) AF: 0.284 AC: 4342 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 782 AN: 3470

East Asian (EAS) AF: 0.547 AC: 2820 AN: 5154

South Asian (SAS) AF: 0.239 AC: 1152 AN: 4824

European-Finnish (FIN) AF: 0.246 AC: 2598 AN: 10572

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14271 AN: 67956

Other (OTH) AF: 0.241 AC: 507 AN: 2106

Alfa AF: 0.214 Hom.: 6069

Bravo AF: 0.218

Asia WGS AF: 0.345 AC: 1196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.8
DANN	Benign	0.19
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1173100; hg19: chr9-93443531;