rs9943849

chr12-68976976-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;