10-4118277-A-C

Variant names:

• chr10-4118277-A-C
• rs1923402
• ENST00000813037.1:n.143+3368T>G

Variant summary

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

The ENST00000813037.1(ENSG00000305807):​n.143+3368T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.914 in 152,044 control chromosomes in the GnomAD database, including 63,561 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 0.91 (63561 hom., cov: 29)
• Consequence: ENSG00000305807 ENST00000813037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 2 publications found

Genes affected

ENSG00000305807 (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 (NFE) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813037.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305807	ENST00000813037.1		n.143+3368T>G		intron	N/A
	ENSG00000305807	ENST00000813038.1		n.162+3368T>G		intron	N/A
	ENSG00000305807	ENST00000813039.1		n.144+3368T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.914 AC: 138866 AN: 151926 Hom.: 63525 Cov.: 29

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.957

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.897

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

GnomAD4 genome AF: 0.914 AC: 138956 AN: 152044 Hom.: 63561 Cov.: 29 AF XY: 0.915 AC XY: 68026 AN XY: 74312

African (AFR) AF: 0.900 AC: 37319 AN: 41444

American (AMR) AF: 0.917 AC: 14015 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2922 AN: 3472

East Asian (EAS) AF: 0.915 AC: 4727 AN: 5164

South Asian (SAS) AF: 0.907 AC: 4362 AN: 4808

European-Finnish (FIN) AF: 0.957 AC: 10141 AN: 10596

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.920 AC: 62544 AN: 67970

Other (OTH) AF: 0.896 AC: 1888 AN: 2108

Alfa AF: 0.911 Hom.: 3796

Bravo AF: 0.909

Asia WGS AF: 0.897 AC: 3119 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	0.34
DANN	Benign	0.71
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs1923402; hg19: chr10-4160469;