12-95470389-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0645

Gnomad4 ASJ AF: 0.0384

Gnomad4 EAS AF: 0.0447

Gnomad4 SAS AF: 0.0815

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.0848

Alfa AF: 0.110 Hom.: 181

Bravo AF: 0.107

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	8.0
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2658718; hg19: chr12-95864165;