chr12-95006862-G-C

Variant names:

• chr12-95006862-G-C
• rs1628439

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 0.183 in 152,028 control chromosomes in the GnomAD database, including 2,625 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 0.18 (2625 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 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: 0.183 AC: 27786 AN: 151910 Hom.: 2622 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.183 AC: 27806 AN: 152028 Hom.: 2625 Cov.: 32 AF XY: 0.177 AC XY: 13138 AN XY: 74312

African (AFR) AF: 0.183 AC: 7600 AN: 41464

American (AMR) AF: 0.136 AC: 2074 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 861 AN: 3468

East Asian (EAS) AF: 0.176 AC: 911 AN: 5178

South Asian (SAS) AF: 0.157 AC: 757 AN: 4814

European-Finnish (FIN) AF: 0.129 AC: 1363 AN: 10548

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13580 AN: 67972

Other (OTH) AF: 0.182 AC: 385 AN: 2116

Alfa AF: 0.190 Hom.: 341

Bravo AF: 0.184

Asia WGS AF: 0.162 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	11
DANN	Benign	0.92
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1628439; hg19: chr12-95400638;