chr9-16901069-C-A

Variant names:

• chr9-16901069-C-A
• rs62543565

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 0.546 in 149,652 control chromosomes in the GnomAD database, including 23,228 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 0.55 (23228 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.62 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: 0.546 AC: 81624 AN: 149542 Hom.: 23219 Cov.: 24

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.546 AC: 81648 AN: 149652 Hom.: 23228 Cov.: 24 AF XY: 0.536 AC XY: 39123 AN XY: 72956

African (AFR) AF: 0.505 AC: 20436 AN: 40498

American (AMR) AF: 0.435 AC: 6541 AN: 15044

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1826 AN: 3452

East Asian (EAS) AF: 0.327 AC: 1573 AN: 4804

South Asian (SAS) AF: 0.230 AC: 1094 AN: 4764

European-Finnish (FIN) AF: 0.597 AC: 6111 AN: 10228

Middle Eastern (MID) AF: 0.524 AC: 151 AN: 288

European-Non Finnish (NFE) AF: 0.625 AC: 42236 AN: 67584

Other (OTH) AF: 0.547 AC: 1139 AN: 2084

Alfa AF: 0.558 Hom.: 2702

Bravo AF: 0.541

Asia WGS AF: 0.288 AC: 1005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.35
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs62543565; hg19: chr9-16901067;