rs1003433

Variant names:

• chr7-12124474-G-T
• rs1003433

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.732 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

Gnomad4 AFR AF: 0.928

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.713

Alfa AF: 0.671 Hom.: 38964

Bravo AF: 0.740

Asia WGS AF: 0.597 AC: 2075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1003433; hg19: chr7-12164100;