chr3-12451848-C-T

Variant names:

• chr3-12451848-C-T
• rs9855622

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 0.115 in 152,246 control chromosomes in the GnomAD database, including 1,028 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 0.12 (1028 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 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: 0.115 AC: 17564 AN: 152128 Hom.: 1029 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.0834

Gnomad SAS AF: 0.0405

Gnomad FIN AF: 0.0968

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.115 AC: 17564 AN: 152246 Hom.: 1028 Cov.: 33 AF XY: 0.113 AC XY: 8413 AN XY: 74428

African (AFR) AF: 0.130 AC: 5392 AN: 41530

American (AMR) AF: 0.113 AC: 1726 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 435 AN: 3472

East Asian (EAS) AF: 0.0832 AC: 431 AN: 5182

South Asian (SAS) AF: 0.0404 AC: 195 AN: 4832

European-Finnish (FIN) AF: 0.0968 AC: 1026 AN: 10598

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8026 AN: 68008

Other (OTH) AF: 0.103 AC: 217 AN: 2114

Alfa AF: 0.117 Hom.: 1823

Bravo AF: 0.118

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.5
DANN	Benign	0.72
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs9855622; hg19: chr3-12493347;