19-45373709-T-C

Variant names:

• chr19-45373709-T-C
• rs11878644

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.524 in 151,856 control chromosomes in the GnomAD database, including 23,571 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 0.52 (23571 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.819 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: 0.523 AC: 79428 AN: 151738 Hom.: 23532 Cov.: 30

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.524 AC: 79523 AN: 151856 Hom.: 23571 Cov.: 30 AF XY: 0.520 AC XY: 38590 AN XY: 74184

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.495

Alfa AF: 0.418 Hom.: 27628

Bravo AF: 0.545

Asia WGS AF: 0.481 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11878644; hg19: chr19-45876967;