12-5040018-A-G

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 0.878 in 152,238 control chromosomes in the GnomAD database, including 58,813 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 0.88 (58813 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.878 AC: 133608 AN: 152120 Hom.: 58773 Cov.: 32

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.878 AC: 133705 AN: 152238 Hom.: 58813 Cov.: 32 AF XY: 0.881 AC XY: 65598 AN XY: 74422

Gnomad4 AFR AF: 0.908

Gnomad4 AMR AF: 0.872

Gnomad4 ASJ AF: 0.902

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.926

Gnomad4 FIN AF: 0.864

Gnomad4 NFE AF: 0.852

Gnomad4 OTH AF: 0.884

Alfa AF: 0.863 Hom.: 17374

Bravo AF: 0.879

Asia WGS AF: 0.957 AC: 3327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	4.7
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7961013; hg19: chr12-5149184;