12-27988699-A-G

Variant names:

• chr12-27988699-A-G
• rs1267209

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 0.983 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.996

Gnomad4 AMR AF: 0.975

Gnomad4 ASJ AF: 0.989

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.984

Gnomad4 FIN AF: 0.990

Gnomad4 NFE AF: 0.985

Gnomad4 OTH AF: 0.982

Alfa AF: 0.985 Hom.: 17036

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1267209; hg19: chr12-28141632;