8-25005194-T-G

Variant summary

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

The ENST00000522570.1(ENSG00000253832):n.350-3200T>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 0.854 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: ENST00000522570.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.93

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379330	XR_949591.2	n.475-3200T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000522570.1	n.350-3200T>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.806

Gnomad4 NFE AF: 0.834

Gnomad4 OTH AF: 0.856

Alfa AF: 0.835 Hom.: 68685

Bravo AF: 0.863

Asia WGS AF: 0.787 AC: 2737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.27
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2950347; hg19: chr8-24862709;