12-37848227-C-T

Variant names:

• chr12-37848227-C-T
• rs12306932

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 0.383 in 149,574 control chromosomes in the GnomAD database, including 12,616 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 0.38 (12616 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.383 AC: 57256 AN: 149456 Hom.: 12618 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.0949

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.383 AC: 57258 AN: 149574 Hom.: 12616 Cov.: 33 AF XY: 0.376 AC XY: 27478 AN XY: 73092

African (AFR) AF: 0.201 AC: 8297 AN: 41196

American (AMR) AF: 0.343 AC: 5124 AN: 14942

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1736 AN: 3402

East Asian (EAS) AF: 0.0952 AC: 488 AN: 5128

South Asian (SAS) AF: 0.339 AC: 1631 AN: 4812

European-Finnish (FIN) AF: 0.417 AC: 4403 AN: 10560

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34138 AN: 66268

Other (OTH) AF: 0.426 AC: 878 AN: 2060

Alfa AF: 0.477 Hom.: 10772

Bravo AF: 0.366

Asia WGS AF: 0.207 AC: 724 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.56

Splicing

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

Other links and lift over

dbSNP: rs12306932; hg19: chr12-38242029;