9-108621858-G-A

Variant names:

• chr9-108621858-G-A
• rs10512355

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 0.408 in 152,122 control chromosomes in the GnomAD database, including 13,094 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 0.41 (13094 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 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: 0.408 AC: 61985 AN: 152004 Hom.: 13087 Cov.: 33

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.408 AC: 62024 AN: 152122 Hom.: 13094 Cov.: 33 AF XY: 0.410 AC XY: 30497 AN XY: 74356

African (AFR) AF: 0.369 AC: 15305 AN: 41504

American (AMR) AF: 0.367 AC: 5603 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1696 AN: 3472

East Asian (EAS) AF: 0.737 AC: 3810 AN: 5170

South Asian (SAS) AF: 0.506 AC: 2438 AN: 4818

European-Finnish (FIN) AF: 0.404 AC: 4267 AN: 10572

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.407 AC: 27656 AN: 67984

Other (OTH) AF: 0.403 AC: 851 AN: 2114

Alfa AF: 0.414 Hom.: 13184

Bravo AF: 0.400

Asia WGS AF: 0.598 AC: 2076 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	0.047
DANN	Benign	0.59
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10512355; hg19: chr9-111384138;