chr12-114554363-G-A

Variant names:

• chr12-114554363-G-A
• rs857748

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.573 in 151,912 control chromosomes in the GnomAD database, including 25,120 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 0.57 (25120 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 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: 0.573 AC: 86974 AN: 151792 Hom.: 25097 Cov.: 31

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.573 AC: 87046 AN: 151912 Hom.: 25120 Cov.: 31 AF XY: 0.570 AC XY: 42315 AN XY: 74246

African (AFR) AF: 0.521 AC: 21592 AN: 41428

American (AMR) AF: 0.603 AC: 9195 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1714 AN: 3468

East Asian (EAS) AF: 0.548 AC: 2817 AN: 5142

South Asian (SAS) AF: 0.561 AC: 2701 AN: 4816

European-Finnish (FIN) AF: 0.552 AC: 5833 AN: 10562

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.607 AC: 41222 AN: 67930

Other (OTH) AF: 0.583 AC: 1228 AN: 2108

Alfa AF: 0.596 Hom.: 29533

Bravo AF: 0.578

Asia WGS AF: 0.538 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	13
DANN	Benign	0.95
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs857748; hg19: chr12-114992168;