chr5-25325828-T-A

Variant names:

• chr5-25325828-T-A
• rs10520926
• ENST00000716652.1:n.107-27219A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000716652.1(ENSG00000248605):​n.107-27219A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,142 control chromosomes in the GnomAD database, including 2,388 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 0.16 (2388 hom., cov: 32)
• Consequence: ENSG00000248605 ENST00000716652.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 3 publications found

Genes affected

ENSG00000248605 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716652.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248605	ENST00000716652.1		n.107-27219A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25066 AN: 152024 Hom.: 2377 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.165 AC: 25097 AN: 152142 Hom.: 2388 Cov.: 32 AF XY: 0.173 AC XY: 12835 AN XY: 74396

African (AFR) AF: 0.111 AC: 4607 AN: 41550

American (AMR) AF: 0.299 AC: 4569 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3468

East Asian (EAS) AF: 0.284 AC: 1467 AN: 5160

South Asian (SAS) AF: 0.266 AC: 1282 AN: 4826

European-Finnish (FIN) AF: 0.170 AC: 1798 AN: 10594

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10132 AN: 67968

Other (OTH) AF: 0.205 AC: 431 AN: 2106

Alfa AF: 0.157 Hom.: 243

Bravo AF: 0.172

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.9
DANN	Benign	0.65
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs10520926; hg19: chr5-25325937;