chr12-131145893-C-T

Variant names:

• chr12-131145893-C-T
• rs7960460

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.45 (13767 hom., cov: 20)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.24).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.544 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: 0.446 AC: 57235 AN: 128198 Hom.: 13762 Cov.: 20

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.446 AC: 57242 AN: 128210 Hom.: 13767 Cov.: 20 AF XY: 0.446 AC XY: 27167 AN XY: 60914

African (AFR) AF: 0.216 AC: 7046 AN: 32568

American (AMR) AF: 0.474 AC: 5784 AN: 12202

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 1874 AN: 3240

East Asian (EAS) AF: 0.355 AC: 1624 AN: 4576

South Asian (SAS) AF: 0.534 AC: 2138 AN: 4006

European-Finnish (FIN) AF: 0.489 AC: 2935 AN: 5998

Middle Eastern (MID) AF: 0.462 AC: 110 AN: 238

European-Non Finnish (NFE) AF: 0.549 AC: 34446 AN: 62790

Other (OTH) AF: 0.447 AC: 777 AN: 1740

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	1.8
DANN	Benign	0.27
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs7960460; hg19: chr12-131630438;