rs43083

Positions:

• chr7-112607132-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;