rs12627816

Variant names:

• chr22-48431879-G-C
• rs12627816

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 0.144 in 152,110 control chromosomes in the GnomAD database, including 1,716 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 0.14 (1716 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

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 = 0.194 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: 0.144 AC: 21911 AN: 151992 Hom.: 1715 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.0576

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.144 AC: 21927 AN: 152110 Hom.: 1716 Cov.: 32 AF XY: 0.146 AC XY: 10898 AN XY: 74404

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.0566

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.162

Alfa AF: 0.125 Hom.: 150

Bravo AF: 0.147

Asia WGS AF: 0.136 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12627816; hg19: chr22-48827691;