chr12-122903375-T-G

Position:

• chr12-122903375-T-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 0.129 in 152,166 control chromosomes in the GnomAD database, including 1,937 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 0.13 (1937 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19605 AN: 152048 Hom.: 1924 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0619

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0337

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0608

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.129 AC: 19660 AN: 152166 Hom.: 1937 Cov.: 31 AF XY: 0.127 AC XY: 9457 AN XY: 74404

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0619

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0337

Gnomad4 NFE AF: 0.0608

Gnomad4 OTH AF: 0.131

Alfa AF: 0.0777 Hom.: 894

Bravo AF: 0.143

Asia WGS AF: 0.181 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10847980; hg19: chr12-123387922;