9-21218097-A-C

Variant names:

• chr9-21218097-A-C
• rs10964912

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 0.194 in 152,022 control chromosomes in the GnomAD database, including 3,590 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 0.19 (3590 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 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: 0.194 AC: 29535 AN: 151904 Hom.: 3596 Cov.: 33

Gnomad AFR AF: 0.0500

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.194 AC: 29531 AN: 152022 Hom.: 3590 Cov.: 33 AF XY: 0.198 AC XY: 14749 AN XY: 74314

African (AFR) AF: 0.0499 AC: 2069 AN: 41498

American (AMR) AF: 0.211 AC: 3214 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 869 AN: 3466

East Asian (EAS) AF: 0.198 AC: 1023 AN: 5178

South Asian (SAS) AF: 0.331 AC: 1595 AN: 4822

European-Finnish (FIN) AF: 0.273 AC: 2880 AN: 10562

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17078 AN: 67940

Other (OTH) AF: 0.219 AC: 464 AN: 2114

Alfa AF: 0.144 Hom.: 347

Bravo AF: 0.183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.51
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs10964912; hg19: chr9-21218096; COSMIC: COSV66510568;