19-53199255-C-T

Position:

• chr19-53199255-C-T

Variant summary

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

The XM_047439805.1(LOC124904792):​c.27+1993C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,016 control chromosomes in the GnomAD database, including 21,656 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 (21656 hom., cov: 32)
• Consequence: LOC124904792 XM_047439805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681

Genes affected

LOC124904792 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904792	XM_047439805.1	c.27+1993C>T		intron_variant			XP_047295761.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000291131	ENST00000597550.5	n.153-1369C>T		intron_variant		4
ENSG00000291131	ENST00000601072.2	n.161+1993C>T		intron_variant		5
ENSG00000291131	ENST00000691047.1	n.151-1369C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79104 AN: 151898 Hom.: 21635 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.521 AC: 79171 AN: 152016 Hom.: 21656 Cov.: 32 AF XY: 0.525 AC XY: 39009 AN XY: 74308

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.530

Alfa AF: 0.566 Hom.: 33408

Bravo AF: 0.513

Asia WGS AF: 0.767 AC: 2667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6509732; hg19: chr19-53702508;