rs12611418

Variant names:

• chr19-388413-A-C
• rs12611418

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 0.214 in 148,594 control chromosomes in the GnomAD database, including 4,634 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 0.21 (4634 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 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: 0.214 AC: 31843 AN: 148478 Hom.: 4629 Cov.: 32

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.289

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.214 AC: 31860 AN: 148594 Hom.: 4634 Cov.: 32 AF XY: 0.216 AC XY: 15665 AN XY: 72572

Gnomad4 AFR AF: 0.0536

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.216

Alfa AF: 0.286 Hom.: 10525

Bravo AF: 0.196

Asia WGS AF: 0.174 AC: 586 AN: 3376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12611418; hg19: chr19-388413;