9-133279871-T-C

Variant names:

• chr9-133279871-T-C
• rs633862

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 0.492 in 151,974 control chromosomes in the GnomAD database, including 18,813 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 0.49 (18813 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.577 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: 0.492 AC: 74771 AN: 151858 Hom.: 18789 Cov.: 31

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.492 AC: 74833 AN: 151974 Hom.: 18813 Cov.: 31 AF XY: 0.493 AC XY: 36642 AN XY: 74274

African (AFR) AF: 0.554 AC: 22935 AN: 41422

American (AMR) AF: 0.587 AC: 8971 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1540 AN: 3472

East Asian (EAS) AF: 0.508 AC: 2631 AN: 5178

South Asian (SAS) AF: 0.452 AC: 2178 AN: 4816

European-Finnish (FIN) AF: 0.408 AC: 4303 AN: 10538

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30877 AN: 67960

Other (OTH) AF: 0.487 AC: 1029 AN: 2112

Alfa AF: 0.414 Hom.: 2179

Bravo AF: 0.513

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs633862; hg19: chr9-136155444;