9-133279427-T-C

Variant names:

• chr9-133279427-T-C
• rs635634

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 0.832 in 152,122 control chromosomes in the GnomAD database, including 52,890 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 0.83 (52890 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 175 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 (AFR) allele frequency at 95% confidence interval = 0.886 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: 0.832 AC: 126436 AN: 152004 Hom.: 52823 Cov.: 31

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.832 AC: 126562 AN: 152122 Hom.: 52890 Cov.: 31 AF XY: 0.834 AC XY: 62001 AN XY: 74338

African (AFR) AF: 0.894 AC: 37112 AN: 41516

American (AMR) AF: 0.849 AC: 12971 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2739 AN: 3470

East Asian (EAS) AF: 0.799 AC: 4120 AN: 5158

South Asian (SAS) AF: 0.849 AC: 4095 AN: 4824

European-Finnish (FIN) AF: 0.791 AC: 8350 AN: 10560

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54686 AN: 68000

Other (OTH) AF: 0.826 AC: 1742 AN: 2110

Alfa AF: 0.833 Hom.: 4633

Bravo AF: 0.837

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.5
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs635634; hg19: chr9-136155000;