12-34021821-G-A

Variant names:

• chr12-34021821-G-A
• rs1705772

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 0.625 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.781 AC: 32369 AN: 41424

American (AMR) AF: 0.514 AC: 7847 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1988 AN: 3468

East Asian (EAS) AF: 0.159 AC: 819 AN: 5166

South Asian (SAS) AF: 0.396 AC: 1909 AN: 4822

European-Finnish (FIN) AF: 0.658 AC: 6945 AN: 10558

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41205 AN: 67952

Other (OTH) AF: 0.575 AC: 1209 AN: 2102

Alfa AF: 0.599 Hom.: 115260

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
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1705772; hg19: chr12-34174756;