chr19-1102140-A-G

Variant names:

• chr19-1102140-A-G
• rs4588110

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 0.536 in 151,920 control chromosomes in the GnomAD database, including 21,938 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 0.54 (21938 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.770
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 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: 0.536 AC: 81333 AN: 151802 Hom.: 21902 Cov.: 33

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.536 AC: 81424 AN: 151920 Hom.: 21938 Cov.: 33 AF XY: 0.544 AC XY: 40392 AN XY: 74260

African (AFR) AF: 0.592 AC: 24522 AN: 41394

American (AMR) AF: 0.585 AC: 8937 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1680 AN: 3470

East Asian (EAS) AF: 0.548 AC: 2826 AN: 5156

South Asian (SAS) AF: 0.551 AC: 2658 AN: 4826

European-Finnish (FIN) AF: 0.608 AC: 6424 AN: 10566

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32512 AN: 67934

Other (OTH) AF: 0.520 AC: 1096 AN: 2106

Alfa AF: 0.533 Hom.: 2825

Bravo AF: 0.534

Asia WGS AF: 0.580 AC: 2015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.68
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs4588110; hg19: chr19-1102139;