chr4-28225806-G-T

Variant names:

• chr4-28225806-G-T
• rs10517138
• ENST00000742923.1:n.222+10658G>T

Variant summary

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

The NR_188396.1(LOC105374557):​n.287+10658G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0591 in 152,182 control chromosomes in the GnomAD database, including 642 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 0.059 (642 hom., cov: 32)
• Consequence: LOC105374557 NR_188396.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 1 publications found

Genes affected

ENSG00000286321 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188396.1. 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
	LOC105374557	NR_188396.1		n.287+10658G>T		intron	N/A
	LOC105374557	NR_188397.1		n.287+10658G>T		intron	N/A
	LOC105374557	NR_188398.1		n.287+10658G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286321	ENST00000742923.1		n.222+10658G>T		intron	N/A
	ENSG00000286321	ENST00000668598.1		n.-163G>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0590 AC: 8976 AN: 152064 Hom.: 644 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0416

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.0801

Gnomad SAS AF: 0.0271

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00595

Gnomad OTH AF: 0.0549

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

GnomAD4 genome AF: 0.0591 AC: 8991 AN: 152182 Hom.: 642 Cov.: 32 AF XY: 0.0589 AC XY: 4386 AN XY: 74412

African (AFR) AF: 0.174 AC: 7207 AN: 41498

American (AMR) AF: 0.0417 AC: 637 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0179 AC: 62 AN: 3468

East Asian (EAS) AF: 0.0799 AC: 413 AN: 5166

South Asian (SAS) AF: 0.0271 AC: 131 AN: 4832

European-Finnish (FIN) AF: 0.000188 AC: 2 AN: 10616

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00597 AC: 406 AN: 68010

Other (OTH) AF: 0.0562 AC: 119 AN: 2116

Alfa AF: 0.0183 Hom.: 48

Bravo AF: 0.0682

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	14
DANN	Benign	0.60
PhyloP100		-0.023

Splicing

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

Other links and lift over

dbSNP: rs10517138; hg19: chr4-28227428;