rs925570

Variant names:

• chr4-22023973-T-C
• rs925570
• ENST00000510705.3:n.446-35111T>C

Variant summary

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

The ENST00000510705.3(ENSG00000250039):​n.446-35111T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,074 control chromosomes in the GnomAD database, including 38,073 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 0.69 (38073 hom., cov: 33)
• Consequence: ENSG00000250039 ENST00000510705.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

ENSG00000250039 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 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
ENSG00000250039	ENST00000510705.3	n.446-35111T>C		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104744 AN: 151956 Hom.: 38053 Cov.: 33

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.689 AC: 104802 AN: 152074 Hom.: 38073 Cov.: 33 AF XY: 0.695 AC XY: 51627 AN XY: 74322

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.704

Alfa AF: 0.700 Hom.: 5584

Bravo AF: 0.678

Asia WGS AF: 0.675 AC: 2349 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	0.48
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs925570; hg19: chr4-22025596;