19-1102132-A-G

Variant names:

• chr19-1102132-A-G
• rs757230

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 151,828 control chromosomes in the GnomAD database, including 21,932 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 (21932 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.587 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: 81319 AN: 151708 Hom.: 21895 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.586

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: 81412 AN: 151828 Hom.: 21932 Cov.: 32 AF XY: 0.544 AC XY: 40376 AN XY: 74200

African (AFR) AF: 0.593 AC: 24531 AN: 41378

American (AMR) AF: 0.586 AC: 8935 AN: 15254

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

East Asian (EAS) AF: 0.548 AC: 2822 AN: 5146

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

European-Finnish (FIN) AF: 0.608 AC: 6417 AN: 10550

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

European-Non Finnish (NFE) AF: 0.479 AC: 32500 AN: 67896

Other (OTH) AF: 0.521 AC: 1098 AN: 2106

Alfa AF: 0.525 Hom.: 2642

Bravo AF: 0.534

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	0.77
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs757230; hg19: chr19-1102131;