rs9474312

Variant names:

• chr6-52733703-C-T
• rs9474312

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 0.491 in 152,088 control chromosomes in the GnomAD database, including 21,500 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 (21500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74666 AN: 151970 Hom.: 21487 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.491 AC: 74698 AN: 152088 Hom.: 21500 Cov.: 32 AF XY: 0.501 AC XY: 37255 AN XY: 74354

African (AFR) AF: 0.174 AC: 7214 AN: 41496

American (AMR) AF: 0.643 AC: 9831 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1668 AN: 3468

East Asian (EAS) AF: 0.710 AC: 3667 AN: 5168

South Asian (SAS) AF: 0.639 AC: 3078 AN: 4820

European-Finnish (FIN) AF: 0.647 AC: 6842 AN: 10570

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40600 AN: 67970

Other (OTH) AF: 0.505 AC: 1064 AN: 2108

Alfa AF: 0.557 Hom.: 18353

Bravo AF: 0.477

Asia WGS AF: 0.634 AC: 2208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.36
DANN	Benign	0.68
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs9474312; hg19: chr6-52598501;