rs803224

Variant names:

• chr5-132870812-G-A
• rs803224

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 0.883 in 152,174 control chromosomes in the GnomAD database, including 60,136 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 0.88 (60136 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.968 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: 0.883 AC: 134209 AN: 152056 Hom.: 60079 Cov.: 31

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.883 AC: 134325 AN: 152174 Hom.: 60136 Cov.: 31 AF XY: 0.871 AC XY: 64773 AN XY: 74362

African (AFR) AF: 0.975 AC: 40528 AN: 41546

American (AMR) AF: 0.783 AC: 11962 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3155 AN: 3470

East Asian (EAS) AF: 0.550 AC: 2835 AN: 5158

South Asian (SAS) AF: 0.871 AC: 4204 AN: 4824

European-Finnish (FIN) AF: 0.701 AC: 7406 AN: 10570

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.901 AC: 61245 AN: 68008

Other (OTH) AF: 0.883 AC: 1862 AN: 2108

Alfa AF: 0.897 Hom.: 31395

Bravo AF: 0.887

Asia WGS AF: 0.710 AC: 2474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.090
DANN	Benign	0.48
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs803224; hg19: chr5-132206504;