4-125889271-A-G

Variant names:

• chr4-125889271-A-G
• rs955806
• ENST00000667497.1:n.164-127046A>G

Variant summary

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

The ENST00000667497.1(ENSG00000250149):​n.164-127046A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,158 control chromosomes in the GnomAD database, including 49,992 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 0.81 (49992 hom., cov: 32)
• Consequence: ENSG00000250149 ENST00000667497.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.807
• Publications: 1 publications found

Genes affected

ENSG00000250149 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667497.1. 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
	ENSG00000250149	ENST00000667497.1		n.164-127046A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122475 AN: 152040 Hom.: 49964 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.805 AC: 122555 AN: 152158 Hom.: 49992 Cov.: 32 AF XY: 0.801 AC XY: 59590 AN XY: 74376

African (AFR) AF: 0.768 AC: 31859 AN: 41506

American (AMR) AF: 0.696 AC: 10636 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2885 AN: 3472

East Asian (EAS) AF: 0.551 AC: 2842 AN: 5156

South Asian (SAS) AF: 0.717 AC: 3460 AN: 4824

European-Finnish (FIN) AF: 0.814 AC: 8631 AN: 10600

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59453 AN: 68008

Other (OTH) AF: 0.801 AC: 1693 AN: 2114

Alfa AF: 0.842 Hom.: 29444

Bravo AF: 0.792

Asia WGS AF: 0.581 AC: 2025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.5
DANN	Benign	0.64
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs955806; hg19: chr4-126810426;