rs10483117

Variant names:

• chr22-25236299-A-G
• rs10483117
• ENST00000757144.1:n.173A>G

Your query was ambiguous. Multiple possible variants found:

• chr22-25236299-A-G
• chr22-25236299-A-T

Variant summary

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

The ENST00000757144.1(ENSG00000298663):​n.173A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,158 control chromosomes in the GnomAD database, including 3,810 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 0.22 (3810 hom., cov: 33)
• Consequence: ENSG00000298663 ENST00000757144.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 3 publications found

Genes affected

ENSG00000298663 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757144.1. 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
	ENSG00000298663	ENST00000757144.1		n.173A>G		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33586 AN: 152038 Hom.: 3804 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.221 AC: 33602 AN: 152158 Hom.: 3810 Cov.: 33 AF XY: 0.223 AC XY: 16558 AN XY: 74392

African (AFR) AF: 0.236 AC: 9806 AN: 41522

American (AMR) AF: 0.194 AC: 2971 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 837 AN: 3468

East Asian (EAS) AF: 0.126 AC: 653 AN: 5172

South Asian (SAS) AF: 0.240 AC: 1160 AN: 4826

European-Finnish (FIN) AF: 0.265 AC: 2806 AN: 10578

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14679 AN: 67976

Other (OTH) AF: 0.224 AC: 474 AN: 2112

Alfa AF: 0.210 Hom.: 5994

Bravo AF: 0.214

Asia WGS AF: 0.208 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.35
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10483117; hg19: chr22-25632266;