12-114231927-G-C

Variant names:

• chr12-114231927-G-C
• rs1920568

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 0.513 in 151,682 control chromosomes in the GnomAD database, including 20,210 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 0.51 (20210 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.587 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: 0.512 AC: 77650 AN: 151564 Hom.: 20168 Cov.: 30

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.513 AC: 77749 AN: 151682 Hom.: 20210 Cov.: 30 AF XY: 0.511 AC XY: 37874 AN XY: 74090

African (AFR) AF: 0.483 AC: 19973 AN: 41332

American (AMR) AF: 0.597 AC: 9115 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1891 AN: 3466

East Asian (EAS) AF: 0.394 AC: 2024 AN: 5134

South Asian (SAS) AF: 0.539 AC: 2584 AN: 4790

European-Finnish (FIN) AF: 0.462 AC: 4844 AN: 10480

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35405 AN: 67918

Other (OTH) AF: 0.518 AC: 1089 AN: 2102

Alfa AF: 0.510 Hom.: 2510

Bravo AF: 0.518

Asia WGS AF: 0.488 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	14
DANN	Benign	0.68
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs1920568; hg19: chr12-114669732;