5-125907327-T-C

Position:

• chr5-125907327-T-C

Variant summary

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

The ENST00000651847.1(ENSG00000248752):​n.472-21569A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 151,926 control chromosomes in the GnomAD database, including 2,014 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 0.14 (2014 hom., cov: 32)
• Consequence: ENST00000651847.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.406

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901056	XR_007058919.1	n.1775-79321A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651847.1	n.472-21569A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21566 AN: 151808 Hom.: 2005 Cov.: 32

Gnomad AFR AF: 0.0683

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.142 AC: 21594 AN: 151926 Hom.: 2014 Cov.: 32 AF XY: 0.145 AC XY: 10777 AN XY: 74270

Gnomad4 AFR AF: 0.0682

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.159

Alfa AF: 0.0168 Hom.: 212

Bravo AF: 0.150

Asia WGS AF: 0.329 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs465384; hg19: chr5-125243020;