12-27988699-A-G

Variant names:

• chr12-27988699-A-G
• rs1267209

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 0.983 in 152,320 control chromosomes in the GnomAD database, including 73,664 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 0.98 (73664 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.988 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: 0.983 AC: 149622 AN: 152202 Hom.: 73608 Cov.: 32

Gnomad AFR AF: 0.996

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.975

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.984

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.982

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

GnomAD4 genome AF: 0.983 AC: 149737 AN: 152320 Hom.: 73664 Cov.: 32 AF XY: 0.983 AC XY: 73230 AN XY: 74470

African (AFR) AF: 0.996 AC: 41406 AN: 41568

American (AMR) AF: 0.975 AC: 14933 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.989 AC: 3434 AN: 3472

East Asian (EAS) AF: 0.849 AC: 4391 AN: 5172

South Asian (SAS) AF: 0.984 AC: 4743 AN: 4822

European-Finnish (FIN) AF: 0.990 AC: 10508 AN: 10616

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.985 AC: 67044 AN: 68036

Other (OTH) AF: 0.982 AC: 2078 AN: 2116

Alfa AF: 0.986 Hom.: 50091

Bravo AF: 0.981

Asia WGS AF: 0.932 AC: 3236 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.3
DANN	Benign	0.60
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1267209; hg19: chr12-28141632;