19-5886721-T-C

Position:

• chr19-5886721-T-C

Variant summary

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

The ENST00000586349.5(ENSG00000267740):​c.382+9732A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 152,178 control chromosomes in the GnomAD database, including 56,397 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 0.86 (56397 hom., cov: 32)
• Consequence: ENSG00000267740 ENST00000586349.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

Genes affected

ENSG00000267740 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.5886721T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000267740	ENST00000586349.5	c.382+9732A>G		intron_variant		2		ENSP00000466639.1
ENSG00000267740	ENST00000585661.1	c.307+9732A>G		intron_variant		2		ENSP00000467210.1
ENSG00000267740	ENST00000592091.5	n.313+9732A>G		intron_variant		2		ENSP00000465499.1

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130824 AN: 152060 Hom.: 56353 Cov.: 32

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.860 AC: 130922 AN: 152178 Hom.: 56397 Cov.: 32 AF XY: 0.858 AC XY: 63841 AN XY: 74386

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.884

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.814

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.866

Alfa AF: 0.870 Hom.: 64796

Bravo AF: 0.868

Asia WGS AF: 0.768 AC: 2674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.79
DANN	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1674159; hg19: chr19-5886732;