rs277230

Variant names:

• chr12-43612413-C-T
• rs277230

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 0.251 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
• Publications: 2 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 (AMR) allele frequency at 95% confidence interval = 0.341 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: 0.251 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

African (AFR) AF: 0.0782 AC: 3248 AN: 41530

American (AMR) AF: 0.348 AC: 5319 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 740 AN: 3470

East Asian (EAS) AF: 0.0387 AC: 200 AN: 5174

South Asian (SAS) AF: 0.243 AC: 1168 AN: 4816

European-Finnish (FIN) AF: 0.319 AC: 3369 AN: 10564

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.342 AC: 23261 AN: 67954

Other (OTH) AF: 0.247 AC: 521 AN: 2112

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
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs277230; hg19: chr12-44006216;