rs10057387

Positions:

• chr5-172803000-T-C

Variant summary

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

The ENST00000702651.1(ENSG00000290019):​n.143T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,978 control chromosomes in the GnomAD database, including 13,445 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 0.42 (13445 hom., cov: 32)
• Consequence: ENSG00000290019 ENST00000702651.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

ENSG00000290019 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.172803000T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290019	ENST00000702651.1	n.143T>C		non_coding_transcript_exon_variant	1/1
ENSG00000290019	ENST00000702508.1	n.124+19T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63683 AN: 151860 Hom.: 13427 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.419 AC: 63741 AN: 151978 Hom.: 13445 Cov.: 32 AF XY: 0.420 AC XY: 31225 AN XY: 74272

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.431

Alfa AF: 0.426 Hom.: 28208

Bravo AF: 0.417

Asia WGS AF: 0.480 AC: 1668 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	0.99
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10057387; hg19: chr5-172230003;