12-88934558-T-C

Variant names:

• chr12-88934558-T-C
• rs12821256

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 0.0685 in 151,976 control chromosomes in the GnomAD database, including 564 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Affects (no stars).

• Frequency: Genomes: 𝑓 0.068 (564 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Affects no assertion criteria provided O:1
• Conservation: PhyloP100: 2.08
• Publications: 87 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 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: 0.0686 AC: 10412 AN: 151860 Hom.: 564 Cov.: 32

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.000388

Gnomad SAS AF: 0.0145

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0685 AC: 10408 AN: 151976 Hom.: 564 Cov.: 32 AF XY: 0.0676 AC XY: 5022 AN XY: 74258

African (AFR) AF: 0.0180 AC: 748 AN: 41542

American (AMR) AF: 0.0285 AC: 434 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3466

East Asian (EAS) AF: 0.000389 AC: 2 AN: 5138

South Asian (SAS) AF: 0.0147 AC: 71 AN: 4826

European-Finnish (FIN) AF: 0.147 AC: 1555 AN: 10594

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7390 AN: 67872

Other (OTH) AF: 0.0436 AC: 92 AN: 2112

Alfa AF: 0.0905 Hom.: 3445

Bravo AF: 0.0579

Asia WGS AF: 0.0140 AC: 47 AN: 3478

ClinVar

ClinVar submissions

Significance: Affects

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	SKIN/HAIR/EYE PIGMENTATION 7, DARK/LIGHT SKIN (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	11
DANN	Benign	0.65
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs12821256; hg19: chr12-89328335;