chr5-172803000-T-C

Variant names:

• chr5-172803000-T-C
• rs10057387
• ENST00000702651.1:n.143T>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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290019	ENST00000702651.1	n.143T>C		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000290019	ENST00000702508.1	n.124+19T>C		intron_variant	Intron 1 of 2

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;