12-95470389-A-G

Variant names:

• chr12-95470389-A-G
• rs2658718

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 0.111 in 151,982 control chromosomes in the GnomAD database, including 979 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 (979 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16807 AN: 151864 Hom.: 981 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.0646

Gnomad ASJ AF: 0.0384

Gnomad EAS AF: 0.0439

Gnomad SAS AF: 0.0816

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.111 AC: 16820 AN: 151982 Hom.: 979 Cov.: 31 AF XY: 0.110 AC XY: 8186 AN XY: 74282

African (AFR) AF: 0.130 AC: 5397 AN: 41468

American (AMR) AF: 0.0645 AC: 984 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0384 AC: 133 AN: 3466

East Asian (EAS) AF: 0.0447 AC: 231 AN: 5164

South Asian (SAS) AF: 0.0815 AC: 392 AN: 4810

European-Finnish (FIN) AF: 0.126 AC: 1325 AN: 10552

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8024 AN: 67946

Other (OTH) AF: 0.0848 AC: 179 AN: 2112

Alfa AF: 0.110 Hom.: 188

Bravo AF: 0.107

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.0
DANN	Benign	0.62
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs2658718; hg19: chr12-95864165;