rs7725052

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 publications found

Genes affected

ENSG00000285616 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648975.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285616	ENST00000648975.1		n.2420+843G>A		intron	N/A
	ENSG00000285552	ENST00000649444.1		n.242+670C>T		intron	N/A
	ENSG00000285552	ENST00000649894.1		n.120-16703C>T		intron	N/A

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

African (AFR) AF: 0.485 AC: 20075 AN: 41432

American (AMR) AF: 0.495 AC: 7553 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1828 AN: 3466

East Asian (EAS) AF: 0.186 AC: 960 AN: 5168

South Asian (SAS) AF: 0.248 AC: 1195 AN: 4824

European-Finnish (FIN) AF: 0.493 AC: 5212 AN: 10562

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39574 AN: 67912

Other (OTH) AF: 0.503 AC: 1058 AN: 2102

Alfa AF: 0.535 Hom.: 6328

Bravo AF: 0.518

Asia WGS AF: 0.237 AC: 825 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	15
DANN	Benign	0.68
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs7725052; hg19: chr5-40487270;