rs815533

Variant names:

• chr3-55441245-A-G
• rs815533

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 0.884 in 152,168 control chromosomes in the GnomAD database, including 59,743 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 (59743 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.962 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: 0.884 AC: 134391 AN: 152050 Hom.: 59685 Cov.: 32

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.861

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.884 AC: 134505 AN: 152168 Hom.: 59743 Cov.: 32 AF XY: 0.886 AC XY: 65874 AN XY: 74374

African (AFR) AF: 0.970 AC: 40279 AN: 41526

American (AMR) AF: 0.896 AC: 13690 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2862 AN: 3470

East Asian (EAS) AF: 0.851 AC: 4393 AN: 5162

South Asian (SAS) AF: 0.879 AC: 4231 AN: 4816

European-Finnish (FIN) AF: 0.894 AC: 9473 AN: 10598

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56706 AN: 68012

Other (OTH) AF: 0.869 AC: 1829 AN: 2104

Alfa AF: 0.850 Hom.: 70208

Bravo AF: 0.888

Asia WGS AF: 0.876 AC: 3044 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.43
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs815533; hg19: chr3-55475273;