8-25005194-T-G

Variant names:

• chr8-25005194-T-G
• rs2950347
• ENST00000522570.1:n.350-3200T>G

Variant summary

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

The ENST00000522570.1(ENSG00000253832):​n.350-3200T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 152,036 control chromosomes in the GnomAD database, including 55,539 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 0.85 (55539 hom., cov: 31)
• Consequence: ENSG00000253832 ENST00000522570.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.93
• Publications: 3 publications found

Genes affected

ENSG00000253832 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522570.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253832	ENST00000522570.1	TSL:3	n.350-3200T>G		intron	N/A
	ENSG00000253832	ENST00000814715.1		n.90-3200T>G		intron	N/A
	ENSG00000253832	ENST00000814716.1		n.78-3200T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129684 AN: 151918 Hom.: 55496 Cov.: 31

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.854 AC: 129784 AN: 152036 Hom.: 55539 Cov.: 31 AF XY: 0.851 AC XY: 63235 AN XY: 74304

African (AFR) AF: 0.909 AC: 37695 AN: 41486

American (AMR) AF: 0.882 AC: 13489 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 2871 AN: 3468

East Asian (EAS) AF: 0.777 AC: 4018 AN: 5168

South Asian (SAS) AF: 0.776 AC: 3727 AN: 4802

European-Finnish (FIN) AF: 0.806 AC: 8496 AN: 10538

Middle Eastern (MID) AF: 0.798 AC: 233 AN: 292

European-Non Finnish (NFE) AF: 0.834 AC: 56719 AN: 67968

Other (OTH) AF: 0.856 AC: 1807 AN: 2112

Alfa AF: 0.844 Hom.: 102176

Bravo AF: 0.863

Asia WGS AF: 0.787 AC: 2737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.39
PhyloP100		-2.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2950347;

hg19: chr8-24862709;