5-142540530-C-T

Position:

• chr5-142540530-C-T

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 0.209 in 151,850 control chromosomes in the GnomAD database, including 5,571 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 0.21 (5571 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.142540530C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPRY4-AS1	ENST00000443800.5	n.244-41272C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31714 AN: 151728 Hom.: 5559 Cov.: 31

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.0875

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0800

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.209 AC: 31763 AN: 151850 Hom.: 5571 Cov.: 31 AF XY: 0.210 AC XY: 15612 AN XY: 74220

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.0875

Gnomad4 NFE AF: 0.0799

Gnomad4 OTH AF: 0.179

Alfa AF: 0.100 Hom.: 1622

Bravo AF: 0.222

Asia WGS AF: 0.379 AC: 1318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs152442; hg19: chr5-141920095;