19-388413-A-C

Variant names:

• chr19-388413-A-C
• rs12611418

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 0.214 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0536 AC: 2190 AN: 40888

American (AMR) AF: 0.152 AC: 2255 AN: 14826

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1466 AN: 3406

East Asian (EAS) AF: 0.200 AC: 936 AN: 4684

South Asian (SAS) AF: 0.248 AC: 1150 AN: 4630

European-Finnish (FIN) AF: 0.320 AC: 3282 AN: 10244

Middle Eastern (MID) AF: 0.296 AC: 84 AN: 284

European-Non Finnish (NFE) AF: 0.297 AC: 19815 AN: 66680

Other (OTH) AF: 0.216 AC: 442 AN: 2046

Alfa AF: 0.274 Hom.: 16554

Bravo AF: 0.196

Asia WGS AF: 0.174 AC: 586 AN: 3376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.56
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs12611418; hg19: chr19-388413;