12-56259911-T-C

Variant names:

• chr12-56259911-T-C
• rs61937678

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.82 (43100 hom., cov: 14)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.952 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: 0.821 AC: 100217 AN: 122102 Hom.: 43108 Cov.: 14

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.958

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.959

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.820 AC: 100222 AN: 122152 Hom.: 43100 Cov.: 14 AF XY: 0.823 AC XY: 47458 AN XY: 57678

African (AFR) AF: 0.495 AC: 15344 AN: 31018

American (AMR) AF: 0.891 AC: 10457 AN: 11734

Ashkenazi Jewish (ASJ) AF: 0.958 AC: 3136 AN: 3274

East Asian (EAS) AF: 0.970 AC: 3930 AN: 4050

South Asian (SAS) AF: 0.979 AC: 3453 AN: 3526

European-Finnish (FIN) AF: 0.959 AC: 5162 AN: 5382

Middle Eastern (MID) AF: 0.942 AC: 226 AN: 240

European-Non Finnish (NFE) AF: 0.931 AC: 56343 AN: 60514

Other (OTH) AF: 0.875 AC: 1409 AN: 1610

Alfa AF: 0.754 Hom.: 1785

Bravo AF: 0.787

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.14
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs61937678; hg19: chr12-56653695;