chr19-11084147-G-A

Variant names:

• chr19-11084147-G-A
• rs11672123

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 0.0369 in 152,254 control chromosomes in the GnomAD database, including 169 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 0.037 (169 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0667 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: 0.0369 AC: 5616 AN: 152136 Hom.: 169 Cov.: 32

Gnomad AFR AF: 0.00806

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0283

Gnomad ASJ AF: 0.0470

Gnomad EAS AF: 0.0724

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.0935

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0463

Gnomad OTH AF: 0.0334

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

GnomAD4 genome AF: 0.0369 AC: 5616 AN: 152254 Hom.: 169 Cov.: 32 AF XY: 0.0390 AC XY: 2904 AN XY: 74436

African (AFR) AF: 0.00804 AC: 334 AN: 41566

American (AMR) AF: 0.0284 AC: 433 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0470 AC: 163 AN: 3470

East Asian (EAS) AF: 0.0727 AC: 377 AN: 5184

South Asian (SAS) AF: 0.0147 AC: 71 AN: 4826

European-Finnish (FIN) AF: 0.0935 AC: 991 AN: 10594

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0464 AC: 3154 AN: 68020

Other (OTH) AF: 0.0326 AC: 69 AN: 2116

Alfa AF: 0.0398 Hom.: 248

Bravo AF: 0.0306

Asia WGS AF: 0.0380 AC: 134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.66
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs11672123; hg19: chr19-11194823;