rs475444

Variant names:

• chr7-54483355-C-T
• rs475444

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 0.715 in 152,048 control chromosomes in the GnomAD database, including 39,738 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 0.71 (39738 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 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: 0.715 AC: 108571 AN: 151932 Hom.: 39713 Cov.: 31

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.715 AC: 108649 AN: 152048 Hom.: 39738 Cov.: 31 AF XY: 0.709 AC XY: 52698 AN XY: 74296

African (AFR) AF: 0.875 AC: 36328 AN: 41512

American (AMR) AF: 0.687 AC: 10495 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2189 AN: 3464

East Asian (EAS) AF: 0.558 AC: 2876 AN: 5154

South Asian (SAS) AF: 0.584 AC: 2806 AN: 4808

European-Finnish (FIN) AF: 0.605 AC: 6395 AN: 10566

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45100 AN: 67950

Other (OTH) AF: 0.724 AC: 1530 AN: 2112

Alfa AF: 0.676 Hom.: 22693

Bravo AF: 0.729

Asia WGS AF: 0.609 AC: 2120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.43
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs475444; hg19: chr7-54551048;