5-53264814-A-G

Variant names:

• chr5-53264814-A-G
• rs38055

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 0.746 in 152,066 control chromosomes in the GnomAD database, including 43,095 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 0.75 (43095 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 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: 0.746 AC: 113371 AN: 151948 Hom.: 43053 Cov.: 31

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.746 AC: 113465 AN: 152066 Hom.: 43095 Cov.: 31 AF XY: 0.744 AC XY: 55299 AN XY: 74348

African (AFR) AF: 0.901 AC: 37375 AN: 41496

American (AMR) AF: 0.716 AC: 10935 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2305 AN: 3470

East Asian (EAS) AF: 0.740 AC: 3815 AN: 5156

South Asian (SAS) AF: 0.669 AC: 3225 AN: 4818

European-Finnish (FIN) AF: 0.718 AC: 7600 AN: 10590

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45787 AN: 67958

Other (OTH) AF: 0.750 AC: 1582 AN: 2108

Alfa AF: 0.696 Hom.: 70971

Bravo AF: 0.760

Asia WGS AF: 0.700 AC: 2433 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.18
DANN	Benign	0.56
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs38055; hg19: chr5-52560644;