rs1003433

Variant names:

• chr7-12124474-G-T
• rs1003433

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 0.732 in 152,072 control chromosomes in the GnomAD database, including 42,002 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 0.73 (42002 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111208 AN: 151954 Hom.: 41937 Cov.: 32

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.732 AC: 111342 AN: 152072 Hom.: 42002 Cov.: 32 AF XY: 0.731 AC XY: 54306 AN XY: 74330

African (AFR) AF: 0.928 AC: 38537 AN: 41530

American (AMR) AF: 0.660 AC: 10080 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2217 AN: 3470

East Asian (EAS) AF: 0.527 AC: 2705 AN: 5136

South Asian (SAS) AF: 0.581 AC: 2793 AN: 4810

European-Finnish (FIN) AF: 0.732 AC: 7737 AN: 10570

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44902 AN: 67960

Other (OTH) AF: 0.713 AC: 1509 AN: 2116

Alfa AF: 0.679 Hom.: 49605

Bravo AF: 0.740

Asia WGS AF: 0.597 AC: 2075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.1
DANN	Benign	0.39
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1003433; hg19: chr7-12164100;