19-45373709-T-C

Variant names:

• chr19-45373709-T-C
• rs11878644

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 0.524 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
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.827 AC: 34254 AN: 41428

American (AMR) AF: 0.449 AC: 6839 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1477 AN: 3468

East Asian (EAS) AF: 0.466 AC: 2402 AN: 5158

South Asian (SAS) AF: 0.436 AC: 2094 AN: 4808

European-Finnish (FIN) AF: 0.399 AC: 4210 AN: 10546

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26588 AN: 67924

Other (OTH) AF: 0.495 AC: 1042 AN: 2106

Alfa AF: 0.433 Hom.: 64583

Bravo AF: 0.545

Asia WGS AF: 0.481 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.45
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs11878644; hg19: chr19-45876967;