rs2227478

Variant names:

• chr12-68254842-A-G
• rs2227478

Your query was ambiguous. Multiple possible variants found:

• chr12-68254842-A-G
• chr12-68254842-A-T

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 0.366 in 152,078 control chromosomes in the GnomAD database, including 10,341 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 0.37 (10341 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.36 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: 0.366 AC: 55577 AN: 151960 Hom.: 10330 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.366 AC: 55622 AN: 152078 Hom.: 10341 Cov.: 32 AF XY: 0.367 AC XY: 27298 AN XY: 74314

African (AFR) AF: 0.364 AC: 15087 AN: 41470

American (AMR) AF: 0.365 AC: 5583 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1547 AN: 3470

East Asian (EAS) AF: 0.197 AC: 1018 AN: 5166

South Asian (SAS) AF: 0.370 AC: 1783 AN: 4818

European-Finnish (FIN) AF: 0.429 AC: 4539 AN: 10578

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.364 AC: 24718 AN: 67988

Other (OTH) AF: 0.398 AC: 839 AN: 2108

Alfa AF: 0.373 Hom.: 30183

Bravo AF: 0.364

Asia WGS AF: 0.333 AC: 1161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.41
PhyloP100		0.067

Splicing

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

Other links and lift over

dbSNP: rs2227478; hg19: chr12-68648622;