rs43083

Variant names:

• chr7-112607132-C-T
• rs43083

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 0.792 in 152,102 control chromosomes in the GnomAD database, including 48,992 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 0.79 (48992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.873 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: 0.792 AC: 120349 AN: 151984 Hom.: 48935 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.792 AC: 120466 AN: 152102 Hom.: 48992 Cov.: 32 AF XY: 0.783 AC XY: 58199 AN XY: 74362

Gnomad4 AFR AF: 0.880

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.845

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.806

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.808

Alfa AF: 0.805 Hom.: 82855

Bravo AF: 0.785

Asia WGS AF: 0.539 AC: 1875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs43083; hg19: chr7-112247187;