rs12673145

Positions:

• chr7-81794147-T-G

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/exons	MANE	UniProt

Ensembl

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