rs12154976

Variant names:

• chr7-120770147-C-T
• rs12154976

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 0.264 in 152,044 control chromosomes in the GnomAD database, including 5,792 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 0.26 (5792 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 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: 0.264 AC: 40177 AN: 151926 Hom.: 5785 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0531

Gnomad SAS AF: 0.0940

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.264 AC: 40211 AN: 152044 Hom.: 5792 Cov.: 32 AF XY: 0.263 AC XY: 19541 AN XY: 74314

African (AFR) AF: 0.356 AC: 14747 AN: 41470

American (AMR) AF: 0.185 AC: 2829 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 612 AN: 3466

East Asian (EAS) AF: 0.0529 AC: 274 AN: 5182

South Asian (SAS) AF: 0.0937 AC: 452 AN: 4824

European-Finnish (FIN) AF: 0.346 AC: 3641 AN: 10534

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16929 AN: 67972

Other (OTH) AF: 0.241 AC: 510 AN: 2114

Alfa AF: 0.241 Hom.: 1774

Bravo AF: 0.258

Asia WGS AF: 0.140 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.94
DANN	Benign	0.34
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs12154976; hg19: chr7-120410201;