rs11668388

chr19-1098810-T-Achr19-1098810-T-G

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 151,918 control chromosomes in the GnomAD database, including 4,023 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 (4023 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.332 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: 0.214 AC: 32497 AN: 151800 Hom.: 4030 Cov.: 31

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.214 AC: 32503 AN: 151918 Hom.: 4023 Cov.: 31 AF XY: 0.218 AC XY: 16145 AN XY: 74224

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.246

Alfa AF: 0.236 Hom.: 571

Bravo AF: 0.215

Asia WGS AF: 0.212 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.0
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11668388; hg19: chr19-1098809;