rs11668388

Variant names:

• chr19-1098810-T-A
• rs11668388

Your query was ambiguous. Multiple possible variants found:

• chr19-1098810-T-A
• chr19-1098810-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;