19-15877610-G-C

Variant names:

• chr19-15877610-G-C
• rs3093209

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 0.288 in 152,034 control chromosomes in the GnomAD database, including 6,855 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 0.29 (6855 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.990
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.39 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: 0.288 AC: 43704 AN: 151916 Hom.: 6847 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.288 AC: 43739 AN: 152034 Hom.: 6855 Cov.: 32 AF XY: 0.288 AC XY: 21370 AN XY: 74324

African (AFR) AF: 0.162 AC: 6720 AN: 41482

American (AMR) AF: 0.304 AC: 4634 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1347 AN: 3468

East Asian (EAS) AF: 0.248 AC: 1272 AN: 5130

South Asian (SAS) AF: 0.405 AC: 1949 AN: 4816

European-Finnish (FIN) AF: 0.298 AC: 3153 AN: 10588

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23561 AN: 67970

Other (OTH) AF: 0.345 AC: 728 AN: 2110

Alfa AF: 0.231 Hom.: 647

Bravo AF: 0.281

Asia WGS AF: 0.345 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.38
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs3093209; hg19: chr19-15988420;