12-49947924-T-C

Variant names:

• chr12-49947924-T-C
• rs296736

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 0.615 in 152,072 control chromosomes in the GnomAD database, including 30,992 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 0.62 (30992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.851 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: 0.615 AC: 93478 AN: 151954 Hom.: 30935 Cov.: 32

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.615 AC: 93590 AN: 152072 Hom.: 30992 Cov.: 32 AF XY: 0.616 AC XY: 45790 AN XY: 74308

African (AFR) AF: 0.859 AC: 35660 AN: 41516

American (AMR) AF: 0.591 AC: 9030 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2228 AN: 3470

East Asian (EAS) AF: 0.777 AC: 4011 AN: 5164

South Asian (SAS) AF: 0.769 AC: 3711 AN: 4824

European-Finnish (FIN) AF: 0.432 AC: 4560 AN: 10546

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32492 AN: 67962

Other (OTH) AF: 0.599 AC: 1265 AN: 2112

Alfa AF: 0.529 Hom.: 37926

Bravo AF: 0.633

Asia WGS AF: 0.790 AC: 2747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
DANN	Benign	0.66
PhyloP100		-0.078

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs296736; hg19: chr12-50341707;