19-50898541-A-G

Variant names:

• chr19-50898541-A-G
• rs8104538

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 152,178 control chromosomes in the GnomAD database, including 6,762 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 (6762 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.694
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 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: 0.289 AC: 43879 AN: 152060 Hom.: 6760 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.0436

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.288 AC: 43900 AN: 152178 Hom.: 6762 Cov.: 32 AF XY: 0.284 AC XY: 21119 AN XY: 74396

African (AFR) AF: 0.277 AC: 11502 AN: 41524

American (AMR) AF: 0.238 AC: 3641 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1560 AN: 3468

East Asian (EAS) AF: 0.0441 AC: 229 AN: 5190

South Asian (SAS) AF: 0.214 AC: 1032 AN: 4818

European-Finnish (FIN) AF: 0.270 AC: 2854 AN: 10580

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21863 AN: 67998

Other (OTH) AF: 0.317 AC: 669 AN: 2108

Alfa AF: 0.310 Hom.: 1566

Bravo AF: 0.287

Asia WGS AF: 0.122 AC: 428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.73
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs8104538; hg19: chr19-51401797;