9-21151554-C-A

Variant names:

• chr9-21151554-C-A
• rs10964862

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 0.348 in 151,972 control chromosomes in the GnomAD database, including 9,470 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 0.35 (9470 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 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: 0.348 AC: 52895 AN: 151854 Hom.: 9458 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.348 AC: 52940 AN: 151972 Hom.: 9470 Cov.: 32 AF XY: 0.349 AC XY: 25903 AN XY: 74294

African (AFR) AF: 0.389 AC: 16109 AN: 41424

American (AMR) AF: 0.315 AC: 4808 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 904 AN: 3466

East Asian (EAS) AF: 0.155 AC: 804 AN: 5180

South Asian (SAS) AF: 0.373 AC: 1794 AN: 4812

European-Finnish (FIN) AF: 0.345 AC: 3637 AN: 10556

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23755 AN: 67948

Other (OTH) AF: 0.333 AC: 702 AN: 2108

Alfa AF: 0.335 Hom.: 13873

Bravo AF: 0.343

Asia WGS AF: 0.290 AC: 1008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.50
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10964862; hg19: chr9-21151553;