rs11672123

chr19-11084147-G-A

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 0.0369 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

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 (EAS) allele frequency at 95% confidence interval = 0.0667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.00804

Gnomad4 AMR AF: 0.0284

Gnomad4 ASJ AF: 0.0470

Gnomad4 EAS AF: 0.0727

Gnomad4 SAS AF: 0.0147

Gnomad4 FIN AF: 0.0935

Gnomad4 NFE AF: 0.0464

Gnomad4 OTH AF: 0.0326

Alfa AF: 0.0422 Hom.: 151

Bravo AF: 0.0306

Asia WGS AF: 0.0380 AC: 134 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	2.3
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11672123; hg19: chr19-11194823;