chr12-67804578-C-T

Variant names:

• chr12-67804578-C-T
• rs2870793

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 0.247 in 152,066 control chromosomes in the GnomAD database, including 4,699 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 0.25 (4699 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37524 AN: 151948 Hom.: 4699 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.247 AC: 37563 AN: 152066 Hom.: 4699 Cov.: 32 AF XY: 0.250 AC XY: 18566 AN XY: 74330

African (AFR) AF: 0.251 AC: 10401 AN: 41476

American (AMR) AF: 0.236 AC: 3604 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 578 AN: 3470

East Asian (EAS) AF: 0.241 AC: 1248 AN: 5172

South Asian (SAS) AF: 0.268 AC: 1289 AN: 4806

European-Finnish (FIN) AF: 0.298 AC: 3155 AN: 10578

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16561 AN: 67978

Other (OTH) AF: 0.218 AC: 459 AN: 2102

Alfa AF: 0.234 Hom.: 6151

Bravo AF: 0.239

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.65
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs2870793; hg19: chr12-68198358;