rs12673145

Variant names:

• chr7-81794147-T-G
• rs12673145

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0147 AC: 612 AN: 41564

American (AMR) AF: 0.0766 AC: 1170 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0354 AC: 123 AN: 3472

East Asian (EAS) AF: 0.176 AC: 913 AN: 5176

South Asian (SAS) AF: 0.0747 AC: 360 AN: 4820

European-Finnish (FIN) AF: 0.0279 AC: 296 AN: 10624

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0324 AC: 2203 AN: 68026

Other (OTH) AF: 0.0402 AC: 85 AN: 2114

Alfa AF: 0.0316 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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs12673145; hg19: chr7-81423463;