9-84667612-C-T

Variant names:

• chr9-84667612-C-T
• rs1212171

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 0.507 in 152,048 control chromosomes in the GnomAD database, including 20,655 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 0.51 (20655 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 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: 0.508 AC: 77112 AN: 151930 Hom.: 20651 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.507 AC: 77136 AN: 152048 Hom.: 20655 Cov.: 32 AF XY: 0.512 AC XY: 38043 AN XY: 74312

African (AFR) AF: 0.322 AC: 13351 AN: 41454

American (AMR) AF: 0.572 AC: 8745 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1949 AN: 3466

East Asian (EAS) AF: 0.584 AC: 3017 AN: 5166

South Asian (SAS) AF: 0.578 AC: 2784 AN: 4814

European-Finnish (FIN) AF: 0.636 AC: 6717 AN: 10554

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38968 AN: 67980

Other (OTH) AF: 0.509 AC: 1076 AN: 2112

Alfa AF: 0.539 Hom.: 52515

Bravo AF: 0.491

Asia WGS AF: 0.505 AC: 1756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.0
DANN	Benign	0.78
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs1212171; hg19: chr9-87282527;