19-18792686-C-G

Variant names:

• chr19-18792686-C-G
• rs730079

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 0.717 in 152,172 control chromosomes in the GnomAD database, including 40,522 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 0.72 (40522 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.89 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: 0.717 AC: 108969 AN: 152054 Hom.: 40459 Cov.: 32

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.717 AC: 109091 AN: 152172 Hom.: 40522 Cov.: 32 AF XY: 0.721 AC XY: 53650 AN XY: 74396

Gnomad4 AFR AF: 0.898

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.642

Alfa AF: 0.681 Hom.: 4515

Bravo AF: 0.719

Asia WGS AF: 0.727 AC: 2529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.5
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs730079; hg19: chr19-18903495;