rs277230

chr12-43612413-C-T

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 0.251 in 152,088 control chromosomes in the GnomAD database, including 6,078 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 0.25 (6078 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.341 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: 0.251 AC: 38207 AN: 151970 Hom.: 6069 Cov.: 32

Gnomad AFR AF: 0.0784

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0388

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.251 AC: 38225 AN: 152088 Hom.: 6078 Cov.: 32 AF XY: 0.250 AC XY: 18598 AN XY: 74330

Gnomad4 AFR AF: 0.0782

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.0387

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.247

Alfa AF: 0.296 Hom.: 977

Bravo AF: 0.252

Asia WGS AF: 0.144 AC: 501 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	2.4
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs277230; hg19: chr12-44006216;