rs7725052

Variant names:

• chr5-40487168-C-T
• rs7725052
• ENST00000648975.1:n.2420+843G>A

Variant summary

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

The ENST00000648975.1(ENSG00000285616):​n.2420+843G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,932 control chromosomes in the GnomAD database, including 20,936 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 0.52 (20936 hom., cov: 32)
• Consequence: ENSG00000285616 ENST00000648975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

Genes affected

ENSG00000285616 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 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
ENSG00000285616	ENST00000648975.1	n.2420+843G>A		intron_variant	Intron 1 of 2
ENSG00000285552	ENST00000649444.1	n.242+670C>T		intron_variant	Intron 2 of 2
ENSG00000285552	ENST00000649894.1	n.120-16703C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78219 AN: 151814 Hom.: 20918 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.515 AC: 78270 AN: 151932 Hom.: 20936 Cov.: 32 AF XY: 0.504 AC XY: 37435 AN XY: 74264

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.503

Alfa AF: 0.549 Hom.: 2878

Bravo AF: 0.518

Asia WGS AF: 0.237 AC: 825 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	15
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7725052; hg19: chr5-40487270;