rs4917589

Variant names:

• chr10-110853044-A-G
• rs4917589
• ENST00000831041.1:n.360+10366A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-110853044-A-G
• chr10-110853044-A-T

Variant summary

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

The ENST00000831041.1(ENSG00000308095):​n.360+10366A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,018 control chromosomes in the GnomAD database, including 46,882 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 0.78 (46882 hom., cov: 30)
• Consequence: ENSG00000308095 ENST00000831041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435
• Publications: 6 publications found

Genes affected

ENSG00000308095 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000831041.1. 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
	ENSG00000308095	ENST00000831041.1		n.360+10366A>G		intron	N/A
	ENSG00000308095	ENST00000831042.1		n.80+541A>G		intron	N/A
	ENSG00000308111	ENST00000831792.1		n.41-103T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118090 AN: 151900 Hom.: 46853 Cov.: 30

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.777 AC: 118160 AN: 152018 Hom.: 46882 Cov.: 30 AF XY: 0.781 AC XY: 58051 AN XY: 74316

African (AFR) AF: 0.602 AC: 24918 AN: 41418

American (AMR) AF: 0.873 AC: 13343 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 3001 AN: 3472

East Asian (EAS) AF: 0.968 AC: 4999 AN: 5162

South Asian (SAS) AF: 0.811 AC: 3910 AN: 4824

European-Finnish (FIN) AF: 0.811 AC: 8583 AN: 10578

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56805 AN: 67964

Other (OTH) AF: 0.776 AC: 1639 AN: 2112

Alfa AF: 0.823 Hom.: 88014

Bravo AF: 0.775

Asia WGS AF: 0.846 AC: 2940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.28
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs4917589; hg19: chr10-112612802;