19-28409075-C-G

Variant names:

• chr19-28409075-C-G
• rs757596

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 0.49 in 151,930 control chromosomes in the GnomAD database, including 20,033 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 0.49 (20033 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 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: 0.490 AC: 74411 AN: 151812 Hom.: 19996 Cov.: 32

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.490 AC: 74512 AN: 151930 Hom.: 20033 Cov.: 32 AF XY: 0.490 AC XY: 36373 AN XY: 74246

African (AFR) AF: 0.719 AC: 29815 AN: 41458

American (AMR) AF: 0.464 AC: 7075 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3466

East Asian (EAS) AF: 0.625 AC: 3222 AN: 5158

South Asian (SAS) AF: 0.288 AC: 1386 AN: 4814

European-Finnish (FIN) AF: 0.432 AC: 4537 AN: 10504

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.378 AC: 25688 AN: 67960

Other (OTH) AF: 0.472 AC: 995 AN: 2110

Alfa AF: 0.277 Hom.: 621

Bravo AF: 0.508

Asia WGS AF: 0.445 AC: 1544 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.35
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs757596; hg19: chr19-28899982;