chr12-23332192-T-C

Variant names:

• chr12-23332192-T-C
• rs7955257

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 0.763 in 152,014 control chromosomes in the GnomAD database, including 45,141 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 0.76 (45141 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 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: 0.763 AC: 115847 AN: 151896 Hom.: 45103 Cov.: 31

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.947

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.763 AC: 115944 AN: 152014 Hom.: 45141 Cov.: 31 AF XY: 0.768 AC XY: 57084 AN XY: 74302

African (AFR) AF: 0.606 AC: 25108 AN: 41428

American (AMR) AF: 0.755 AC: 11517 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.947 AC: 3287 AN: 3472

East Asian (EAS) AF: 0.956 AC: 4937 AN: 5166

South Asian (SAS) AF: 0.919 AC: 4426 AN: 4816

European-Finnish (FIN) AF: 0.820 AC: 8676 AN: 10580

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.813 AC: 55241 AN: 67984

Other (OTH) AF: 0.784 AC: 1657 AN: 2114

Alfa AF: 0.776 Hom.: 8278

Bravo AF: 0.754

Asia WGS AF: 0.897 AC: 3119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.11
DANN	Benign	0.57
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs7955257; hg19: chr12-23485126;