rs7634533

Variant names:

• chr3-30330561-C-A
• rs7634533

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 0.352 in 151,692 control chromosomes in the GnomAD database, including 9,572 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 0.35 (9572 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53408 AN: 151574 Hom.: 9571 Cov.: 31

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.352 AC: 53439 AN: 151692 Hom.: 9572 Cov.: 31 AF XY: 0.354 AC XY: 26206 AN XY: 74128

African (AFR) AF: 0.384 AC: 15879 AN: 41380

American (AMR) AF: 0.454 AC: 6902 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1193 AN: 3460

East Asian (EAS) AF: 0.332 AC: 1709 AN: 5140

South Asian (SAS) AF: 0.370 AC: 1780 AN: 4816

European-Finnish (FIN) AF: 0.325 AC: 3431 AN: 10544

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.314 AC: 21332 AN: 67844

Other (OTH) AF: 0.339 AC: 715 AN: 2110

Alfa AF: 0.329 Hom.: 15587

Bravo AF: 0.365

Asia WGS AF: 0.373 AC: 1300 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	8.8
DANN	Benign	0.56
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs7634533; hg19: chr3-30372053;