rs503283

Variant names:

• chr13-68454349-A-G
• rs503283

Your query was ambiguous. Multiple possible variants found:

• chr13-68454349-A-G
• chr13-68454349-A-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 0.164 in 152,036 control chromosomes in the GnomAD database, including 2,360 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 0.16 (2360 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713
• Publications: 3 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 = 0.253 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: 0.164 AC: 24894 AN: 151920 Hom.: 2348 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.164 AC: 24955 AN: 152036 Hom.: 2360 Cov.: 32 AF XY: 0.164 AC XY: 12217 AN XY: 74314

African (AFR) AF: 0.257 AC: 10650 AN: 41476

American (AMR) AF: 0.200 AC: 3049 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 666 AN: 3470

East Asian (EAS) AF: 0.159 AC: 823 AN: 5170

South Asian (SAS) AF: 0.172 AC: 828 AN: 4820

European-Finnish (FIN) AF: 0.0753 AC: 798 AN: 10602

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7522 AN: 67964

Other (OTH) AF: 0.161 AC: 339 AN: 2110

Alfa AF: 0.131 Hom.: 5349

Bravo AF: 0.178

Asia WGS AF: 0.195 AC: 678 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs503283; hg19: chr13-69028481;