12-61569192-C-T

Variant names:

• chr12-61569192-C-T
• rs2048078

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 0.455 in 151,980 control chromosomes in the GnomAD database, including 16,459 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 0.45 (16459 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.525 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: 0.455 AC: 69094 AN: 151862 Hom.: 16462 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.455 AC: 69108 AN: 151980 Hom.: 16459 Cov.: 33 AF XY: 0.454 AC XY: 33692 AN XY: 74278

African (AFR) AF: 0.305 AC: 12655 AN: 41480

American (AMR) AF: 0.525 AC: 8017 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1773 AN: 3470

East Asian (EAS) AF: 0.353 AC: 1821 AN: 5164

South Asian (SAS) AF: 0.434 AC: 2094 AN: 4820

European-Finnish (FIN) AF: 0.483 AC: 5090 AN: 10546

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.530 AC: 35971 AN: 67924

Other (OTH) AF: 0.485 AC: 1023 AN: 2110

Alfa AF: 0.509 Hom.: 24458

Bravo AF: 0.453

Asia WGS AF: 0.410 AC: 1424 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.57
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2048078; hg19: chr12-61962973;