rs7132980

Variant names:

• chr12-25265143-A-G
• rs7132980

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 0.292 in 152,084 control chromosomes in the GnomAD database, including 6,697 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 0.29 (6697 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.479
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.336 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: 0.292 AC: 44414 AN: 151966 Hom.: 6684 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.292 AC: 44455 AN: 152084 Hom.: 6697 Cov.: 32 AF XY: 0.292 AC XY: 21726 AN XY: 74336

African (AFR) AF: 0.200 AC: 8281 AN: 41504

American (AMR) AF: 0.344 AC: 5254 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1058 AN: 3472

East Asian (EAS) AF: 0.292 AC: 1510 AN: 5176

South Asian (SAS) AF: 0.216 AC: 1040 AN: 4816

European-Finnish (FIN) AF: 0.329 AC: 3473 AN: 10566

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22952 AN: 67968

Other (OTH) AF: 0.299 AC: 631 AN: 2112

Alfa AF: 0.325 Hom.: 10325

Bravo AF: 0.294

Asia WGS AF: 0.277 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.8
DANN	Benign	0.86
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs7132980; hg19: chr12-25418077;