chr12-68976976-C-T

Variant names:

• chr12-68976976-C-T
• rs9943849

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.262 in 152,114 control chromosomes in the GnomAD database, including 5,453 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 0.26 (5453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39866 AN: 151996 Hom.: 5442 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.262 AC: 39918 AN: 152114 Hom.: 5453 Cov.: 32 AF XY: 0.260 AC XY: 19370 AN XY: 74362

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.241

Alfa AF: 0.242 Hom.: 9774

Bravo AF: 0.260

Asia WGS AF: 0.284 AC: 985 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.94
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9943849; hg19: chr12-69370756;