chr9-108488066-T-C

Variant names:

• chr9-108488066-T-C
• rs1924219

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 0.282 in 152,094 control chromosomes in the GnomAD database, including 7,140 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 0.28 (7140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 4 publications found

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 (AMR) allele frequency at 95% confidence interval = 0.37 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: 0.282 AC: 42927 AN: 151976 Hom.: 7129 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.0357

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.282 AC: 42947 AN: 152094 Hom.: 7140 Cov.: 32 AF XY: 0.282 AC XY: 20970 AN XY: 74326

African (AFR) AF: 0.115 AC: 4772 AN: 41518

American (AMR) AF: 0.378 AC: 5783 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1426 AN: 3472

East Asian (EAS) AF: 0.0352 AC: 182 AN: 5170

South Asian (SAS) AF: 0.311 AC: 1494 AN: 4808

European-Finnish (FIN) AF: 0.372 AC: 3924 AN: 10550

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.357 AC: 24246 AN: 67970

Other (OTH) AF: 0.344 AC: 725 AN: 2108

Alfa AF: 0.338 Hom.: 5091

Bravo AF: 0.277

Asia WGS AF: 0.203 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.83
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1924219; hg19: chr9-111250346;