12-112554573-T-C

Variant names:

• chr12-112554573-T-C
• rs3858706

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 0.348 in 151,808 control chromosomes in the GnomAD database, including 11,797 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 0.35 (11797 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.89
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.86 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: 0.348 AC: 52782 AN: 151692 Hom.: 11783 Cov.: 31

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.348 AC: 52854 AN: 151808 Hom.: 11797 Cov.: 31 AF XY: 0.358 AC XY: 26578 AN XY: 74196

African (AFR) AF: 0.536 AC: 22147 AN: 41316

American (AMR) AF: 0.349 AC: 5321 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3468

East Asian (EAS) AF: 0.881 AC: 4543 AN: 5156

South Asian (SAS) AF: 0.608 AC: 2927 AN: 4816

European-Finnish (FIN) AF: 0.223 AC: 2354 AN: 10538

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14230 AN: 67946

Other (OTH) AF: 0.327 AC: 691 AN: 2112

Alfa AF: 0.280 Hom.: 922

Bravo AF: 0.367

Asia WGS AF: 0.681 AC: 2365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.36
DANN	Benign	0.31
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs3858706; hg19: chr12-112992377;