rs1033059

Variant names:

• chr3-162072644-A-G
• rs1033059

Your query was ambiguous. Multiple possible variants found:

• chr3-162072644-A-G
• chr3-162072644-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 0.194 in 152,140 control chromosomes in the GnomAD database, including 3,871 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 0.19 (3871 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 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: 0.195 AC: 29590 AN: 152022 Hom.: 3871 Cov.: 32

Gnomad AFR AF: 0.0509

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.00790

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.194 AC: 29585 AN: 152140 Hom.: 3871 Cov.: 32 AF XY: 0.192 AC XY: 14274 AN XY: 74362

African (AFR) AF: 0.0507 AC: 2107 AN: 41542

American (AMR) AF: 0.133 AC: 2038 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3472

East Asian (EAS) AF: 0.00811 AC: 42 AN: 5180

South Asian (SAS) AF: 0.175 AC: 845 AN: 4818

European-Finnish (FIN) AF: 0.323 AC: 3404 AN: 10542

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19906 AN: 67984

Other (OTH) AF: 0.174 AC: 367 AN: 2114

Alfa AF: 0.253 Hom.: 709

Bravo AF: 0.171

Asia WGS AF: 0.0800 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.61
DANN	Benign	0.62
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1033059; hg19: chr3-161790432;