rs2168029

Variant names:

• chr12-69340861-A-C
• rs2168029

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 0.426 in 152,034 control chromosomes in the GnomAD database, including 16,040 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 0.43 (16040 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343
• Publications: 35 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 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: 0.427 AC: 64813 AN: 151916 Hom.: 16034 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.426 AC: 64829 AN: 152034 Hom.: 16040 Cov.: 32 AF XY: 0.430 AC XY: 31985 AN XY: 74312

African (AFR) AF: 0.170 AC: 7041 AN: 41498

American (AMR) AF: 0.509 AC: 7787 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3472

East Asian (EAS) AF: 0.713 AC: 3677 AN: 5160

South Asian (SAS) AF: 0.672 AC: 3242 AN: 4824

European-Finnish (FIN) AF: 0.433 AC: 4571 AN: 10546

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35284 AN: 67932

Other (OTH) AF: 0.453 AC: 954 AN: 2106

Alfa AF: 0.488 Hom.: 60029

Bravo AF: 0.416

Asia WGS AF: 0.644 AC: 2238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.43
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2168029; hg19: chr12-69734641;