chr19-15639993-A-G

Variant names:

• chr19-15639993-A-G
• rs1159776

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 0.198 in 152,028 control chromosomes in the GnomAD database, including 3,576 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 0.20 (3576 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 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: 0.198 AC: 30084 AN: 151910 Hom.: 3576 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.198 AC: 30105 AN: 152028 Hom.: 3576 Cov.: 31 AF XY: 0.198 AC XY: 14704 AN XY: 74302

African (AFR) AF: 0.326 AC: 13492 AN: 41426

American (AMR) AF: 0.146 AC: 2231 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3470

East Asian (EAS) AF: 0.193 AC: 996 AN: 5158

South Asian (SAS) AF: 0.121 AC: 582 AN: 4810

European-Finnish (FIN) AF: 0.179 AC: 1890 AN: 10584

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9732 AN: 67986

Other (OTH) AF: 0.171 AC: 360 AN: 2108

Alfa AF: 0.169 Hom.: 5195

Bravo AF: 0.203

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.2
DANN	Benign	0.79
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1159776; hg19: chr19-15750803;