chr12-102786158-A-C

Variant names:

• chr12-102786158-A-C
• rs1722400

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 0.201 in 152,100 control chromosomes in the GnomAD database, including 3,817 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 0.20 (3817 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 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: 0.201 AC: 30579 AN: 151982 Hom.: 3805 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00559

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0898

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.201 AC: 30627 AN: 152100 Hom.: 3817 Cov.: 32 AF XY: 0.197 AC XY: 14644 AN XY: 74364

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.00541

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0898

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.177

Alfa AF: 0.169 Hom.: 518

Bravo AF: 0.223

Asia WGS AF: 0.0830 AC: 290 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.6
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1722400; hg19: chr12-103179936;