chr19-1098067-A-G

Variant names:

• chr19-1098067-A-G
• rs10439143

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 0.568 in 151,976 control chromosomes in the GnomAD database, including 25,538 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 0.57 (25538 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.50
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86260 AN: 151858 Hom.: 25505 Cov.: 32

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.568 AC: 86353 AN: 151976 Hom.: 25538 Cov.: 32 AF XY: 0.573 AC XY: 42567 AN XY: 74276

African (AFR) AF: 0.681 AC: 28221 AN: 41436

American (AMR) AF: 0.654 AC: 9979 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1971 AN: 3472

East Asian (EAS) AF: 0.791 AC: 4074 AN: 5152

South Asian (SAS) AF: 0.668 AC: 3221 AN: 4820

European-Finnish (FIN) AF: 0.451 AC: 4762 AN: 10568

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.473 AC: 32151 AN: 67958

Other (OTH) AF: 0.586 AC: 1235 AN: 2106

Alfa AF: 0.516 Hom.: 26142

Bravo AF: 0.586

Asia WGS AF: 0.694 AC: 2411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.076
DANN	Benign	0.32
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs10439143; hg19: chr19-1098066;