chr9-85315130-A-C

Variant names:

• chr9-85315130-A-C
• rs2841498

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 0.859 in 152,220 control chromosomes in the GnomAD database, including 56,541 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 0.86 (56541 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839
• Publications: 9 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 (AFR) allele frequency at 95% confidence interval = 0.948 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: 0.858 AC: 130572 AN: 152102 Hom.: 56479 Cov.: 33

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.860

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.859 AC: 130692 AN: 152220 Hom.: 56541 Cov.: 33 AF XY: 0.856 AC XY: 63708 AN XY: 74424

African (AFR) AF: 0.955 AC: 39685 AN: 41538

American (AMR) AF: 0.750 AC: 11461 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 3028 AN: 3472

East Asian (EAS) AF: 0.947 AC: 4901 AN: 5174

South Asian (SAS) AF: 0.890 AC: 4297 AN: 4826

European-Finnish (FIN) AF: 0.794 AC: 8405 AN: 10592

Middle Eastern (MID) AF: 0.856 AC: 250 AN: 292

European-Non Finnish (NFE) AF: 0.827 AC: 56232 AN: 68024

Other (OTH) AF: 0.864 AC: 1823 AN: 2110

Alfa AF: 0.839 Hom.: 185674

Bravo AF: 0.858

Asia WGS AF: 0.923 AC: 3210 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	0.36
DANN	Benign	0.45
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs2841498; hg19: chr9-87930045;