rs925570

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000250039 (HGNC:58742):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.432 AC: 17931 AN: 41464

American (AMR) AF: 0.770 AC: 11770 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2762 AN: 3472

East Asian (EAS) AF: 0.798 AC: 4102 AN: 5140

South Asian (SAS) AF: 0.672 AC: 3237 AN: 4818

European-Finnish (FIN) AF: 0.818 AC: 8662 AN: 10588

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53998 AN: 67990

Other (OTH) AF: 0.704 AC: 1489 AN: 2116

Alfa AF: 0.692 Hom.: 5661

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs925570; hg19: chr4-22025596;