chr12-34021821-G-A

Position:

• chr12-34021821-G-A

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 0.625 in 151,954 control chromosomes in the GnomAD database, including 31,169 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 0.63 (31169 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 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: 0.625 AC: 94916 AN: 151836 Hom.: 31124 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.625 AC: 95010 AN: 151954 Hom.: 31169 Cov.: 32 AF XY: 0.620 AC XY: 46041 AN XY: 74244

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.575

Alfa AF: 0.591 Hom.: 53796

Bravo AF: 0.623

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.16
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1705772; hg19: chr12-34174756;