12-68806705-A-G

Variant names:

• chr12-68806705-A-G
• rs1144944

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 0.562 in 151,876 control chromosomes in the GnomAD database, including 26,910 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 0.56 (26910 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• 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 (AFR) allele frequency at 95% confidence interval = 0.855 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: 0.561 AC: 85203 AN: 151758 Hom.: 26850 Cov.: 30

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.562 AC: 85330 AN: 151876 Hom.: 26910 Cov.: 30 AF XY: 0.551 AC XY: 40872 AN XY: 74194

African (AFR) AF: 0.863 AC: 35763 AN: 41442

American (AMR) AF: 0.373 AC: 5687 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1265 AN: 3464

East Asian (EAS) AF: 0.296 AC: 1527 AN: 5164

South Asian (SAS) AF: 0.313 AC: 1507 AN: 4814

European-Finnish (FIN) AF: 0.457 AC: 4812 AN: 10522

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.487 AC: 33085 AN: 67916

Other (OTH) AF: 0.507 AC: 1066 AN: 2104

Alfa AF: 0.531 Hom.: 2786

Bravo AF: 0.571

Asia WGS AF: 0.362 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.69
DANN	Benign	0.33
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1144944; hg19: chr12-69200485;