rs12673145

Variant names:

• chr7-81794147-T-G
• rs12673145

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 0.0381 in 152,274 control chromosomes in the GnomAD database, including 224 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 0.038 (224 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

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 (EAS) allele frequency at 95% confidence interval = 0.167 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: 0.0381 AC: 5793 AN: 152154 Hom.: 224 Cov.: 32

Gnomad AFR AF: 0.0147

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0764

Gnomad ASJ AF: 0.0354

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.0740

Gnomad FIN AF: 0.0279

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0324

Gnomad OTH AF: 0.0387

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

GnomAD4 genome AF: 0.0381 AC: 5802 AN: 152274 Hom.: 224 Cov.: 32 AF XY: 0.0403 AC XY: 3002 AN XY: 74436

Gnomad4 AFR AF: 0.0147

Gnomad4 AMR AF: 0.0766

Gnomad4 ASJ AF: 0.0354

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.0747

Gnomad4 FIN AF: 0.0279

Gnomad4 NFE AF: 0.0324

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0320 Hom.: 16

Bravo AF: 0.0420

Asia WGS AF: 0.124 AC: 428 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	2.2
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: rs12673145; hg19: chr7-81423463;