12-90485328-T-C

Variant names:

• chr12-90485328-T-C
• rs6538238

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 0.519 in 149,842 control chromosomes in the GnomAD database, including 23,742 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 0.52 (23742 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 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: 0.519 AC: 77772 AN: 149776 Hom.: 23708 Cov.: 30

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.273

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.519 AC: 77842 AN: 149842 Hom.: 23742 Cov.: 30 AF XY: 0.515 AC XY: 37626 AN XY: 73126

African (AFR) AF: 0.844 AC: 34587 AN: 40982

American (AMR) AF: 0.468 AC: 7018 AN: 14996

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 981 AN: 3466

East Asian (EAS) AF: 0.685 AC: 3521 AN: 5142

South Asian (SAS) AF: 0.442 AC: 2118 AN: 4794

European-Finnish (FIN) AF: 0.328 AC: 3132 AN: 9560

Middle Eastern (MID) AF: 0.271 AC: 77 AN: 284

European-Non Finnish (NFE) AF: 0.371 AC: 25059 AN: 67618

Other (OTH) AF: 0.460 AC: 961 AN: 2088

Alfa AF: 0.283 Hom.: 740

Bravo AF: 0.543

Asia WGS AF: 0.634 AC: 2202 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.20
DANN	Benign	0.41
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs6538238; hg19: chr12-90879105;