12-23278623-T-G

Variant names:

• chr12-23278623-T-G
• rs4321001

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 0.872 in 152,136 control chromosomes in the GnomAD database, including 59,755 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 0.87 (59755 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.872 AC: 132542 AN: 152018 Hom.: 59725 Cov.: 31

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.949

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.977

Gnomad OTH AF: 0.890

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

GnomAD4 genome AF: 0.872 AC: 132620 AN: 152136 Hom.: 59755 Cov.: 31 AF XY: 0.875 AC XY: 65045 AN XY: 74366

African (AFR) AF: 0.615 AC: 25478 AN: 41444

American (AMR) AF: 0.930 AC: 14227 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.949 AC: 3290 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5143 AN: 5152

South Asian (SAS) AF: 0.948 AC: 4570 AN: 4822

European-Finnish (FIN) AF: 0.983 AC: 10428 AN: 10612

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.977 AC: 66479 AN: 68030

Other (OTH) AF: 0.891 AC: 1880 AN: 2110

Alfa AF: 0.937 Hom.: 34300

Bravo AF: 0.857

Asia WGS AF: 0.940 AC: 3269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.56
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs4321001; hg19: chr12-23431557;