rs12537284

Variant names:

• chr7-129077852-G-A
• rs12537284

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 0.107 in 152,158 control chromosomes in the GnomAD database, including 1,171 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 0.11 (1171 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.678
• Publications: 56 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16244 AN: 152042 Hom.: 1172 Cov.: 33

Gnomad AFR AF: 0.0317

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.107 AC: 16245 AN: 152158 Hom.: 1171 Cov.: 33 AF XY: 0.109 AC XY: 8104 AN XY: 74368

African (AFR) AF: 0.0317 AC: 1318 AN: 41516

American (AMR) AF: 0.159 AC: 2429 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3472

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5174

South Asian (SAS) AF: 0.154 AC: 743 AN: 4828

European-Finnish (FIN) AF: 0.159 AC: 1681 AN: 10560

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9141 AN: 67992

Other (OTH) AF: 0.123 AC: 261 AN: 2114

Alfa AF: 0.124 Hom.: 4597

Bravo AF: 0.104

Asia WGS AF: 0.0650 AC: 225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.9
DANN	Benign	0.48
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs12537284; hg19: chr7-128717906;