chr19-1098810-T-A

Variant names:

• chr19-1098810-T-A
• rs11668388

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 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
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• 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

African (AFR) AF: 0.102 AC: 4233 AN: 41438

American (AMR) AF: 0.340 AC: 5189 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1125 AN: 3470

East Asian (EAS) AF: 0.163 AC: 841 AN: 5172

South Asian (SAS) AF: 0.272 AC: 1308 AN: 4808

European-Finnish (FIN) AF: 0.242 AC: 2556 AN: 10564

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16379 AN: 67886

Other (OTH) AF: 0.246 AC: 518 AN: 2104

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
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs11668388; hg19: chr19-1098809;