rs503022

Variant names:

• chr3-55457408-C-A
• rs503022

Your query was ambiguous. Multiple possible variants found:

• chr3-55457408-C-A
• chr3-55457408-C-T

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 0.155 in 152,134 control chromosomes in the GnomAD database, including 2,057 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 0.15 (2057 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 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: 0.155 AC: 23511 AN: 152016 Hom.: 2054 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.0729

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0954

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.155 AC: 23528 AN: 152134 Hom.: 2057 Cov.: 32 AF XY: 0.150 AC XY: 11165 AN XY: 74402

African (AFR) AF: 0.236 AC: 9781 AN: 41468

American (AMR) AF: 0.114 AC: 1738 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 696 AN: 3472

East Asian (EAS) AF: 0.0729 AC: 377 AN: 5172

South Asian (SAS) AF: 0.100 AC: 484 AN: 4820

European-Finnish (FIN) AF: 0.0954 AC: 1010 AN: 10592

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8892 AN: 68004

Other (OTH) AF: 0.161 AC: 340 AN: 2112

Alfa AF: 0.135 Hom.: 3011

Bravo AF: 0.161

Asia WGS AF: 0.0980 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.73
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs503022; hg19: chr3-55491436;