rs12673563

chr7-91651155-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 0.138 in 152,092 control chromosomes in the GnomAD database, including 1,736 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 0.14 (1736 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 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: 0.138 AC: 20965 AN: 151974 Hom.: 1727 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.0992

Gnomad SAS AF: 0.0583

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0984

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.138 AC: 20998 AN: 152092 Hom.: 1736 Cov.: 32 AF XY: 0.135 AC XY: 10030 AN XY: 74366

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.0732

Gnomad4 EAS AF: 0.0992

Gnomad4 SAS AF: 0.0579

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0984

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0986 Hom.: 923

Bravo AF: 0.146

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	7.3
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12673563; hg19: chr7-91280470;