19-44018761-C-T

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 0.53 in 152,000 control chromosomes in the GnomAD database, including 24,759 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 0.53 (24759 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.402

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80522 AN: 151882 Hom.: 24762 Cov.: 31

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.530 AC: 80515 AN: 152000 Hom.: 24759 Cov.: 31 AF XY: 0.527 AC XY: 39180 AN XY: 74290

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.546

Alfa AF: 0.657 Hom.: 35779

Bravo AF: 0.487

Asia WGS AF: 0.441 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.6
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6509133; hg19: chr19-44522913;