19-44924096-C-G

Variant names:

• chr19-44924096-C-G
• rs4803770

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 0.332 in 151,792 control chromosomes in the GnomAD database, including 8,580 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 0.33 (8580 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.378 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: 0.332 AC: 50323 AN: 151672 Hom.: 8583 Cov.: 31

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.332 AC: 50335 AN: 151792 Hom.: 8580 Cov.: 31 AF XY: 0.329 AC XY: 24413 AN XY: 74152

African (AFR) AF: 0.261 AC: 10794 AN: 41390

American (AMR) AF: 0.303 AC: 4610 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1221 AN: 3464

East Asian (EAS) AF: 0.210 AC: 1083 AN: 5166

South Asian (SAS) AF: 0.274 AC: 1318 AN: 4808

European-Finnish (FIN) AF: 0.389 AC: 4098 AN: 10528

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25938 AN: 67904

Other (OTH) AF: 0.361 AC: 759 AN: 2102

Alfa AF: 0.230 Hom.: 519

Bravo AF: 0.323

Asia WGS AF: 0.234 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.58
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs4803770; hg19: chr19-45427353;