5-1359823-T-C

Position:

• chr5-1359823-T-C

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 0.84 in 152,236 control chromosomes in the GnomAD database, including 53,891 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 0.84 (53891 hom., cov: 34)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.1359823T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01511	ENST00000653645.1	n.437-4288A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127794 AN: 152118 Hom.: 53867 Cov.: 34

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.840 AC: 127873 AN: 152236 Hom.: 53891 Cov.: 34 AF XY: 0.838 AC XY: 62365 AN XY: 74420

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.888

Gnomad4 NFE AF: 0.871

Gnomad4 OTH AF: 0.833

Alfa AF: 0.857 Hom.: 24922

Bravo AF: 0.835

Asia WGS AF: 0.779 AC: 2707 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	0.79
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: rs27064; hg19: chr5-1359938;