rs10483134

Variant names:

• chr22-27351290-A-G
• rs10483134
• ENST00000413244.1:n.491+15028A>G

Variant summary

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

The ENST00000413244.1(ENSG00000230051):​n.491+15028A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,164 control chromosomes in the GnomAD database, including 2,590 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 0.17 (2590 hom., cov: 33)
• Consequence: ENSG00000230051 ENST00000413244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 0 publications found

Genes affected

ENSG00000230051 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724900	XR_430432.4	n.711-6183A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230051	ENST00000413244.1	n.491+15028A>G		intron_variant	Intron 3 of 3	4
ENSG00000230051	ENST00000668323.1	n.1167-6183A>G		intron_variant	Intron 4 of 4
ENSG00000230051	ENST00000669277.3	n.634-6183A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26570 AN: 152046 Hom.: 2592 Cov.: 33

Gnomad AFR AF: 0.0998

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.0656

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.175 AC: 26566 AN: 152164 Hom.: 2590 Cov.: 33 AF XY: 0.171 AC XY: 12706 AN XY: 74376

African (AFR) AF: 0.0996 AC: 4136 AN: 41534

American (AMR) AF: 0.130 AC: 1995 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 539 AN: 3466

East Asian (EAS) AF: 0.0652 AC: 338 AN: 5184

South Asian (SAS) AF: 0.207 AC: 995 AN: 4818

European-Finnish (FIN) AF: 0.212 AC: 2237 AN: 10574

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15765 AN: 67980

Other (OTH) AF: 0.180 AC: 381 AN: 2114

Alfa AF: 0.197 Hom.: 396

Bravo AF: 0.163

Asia WGS AF: 0.139 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.5
DANN	Benign	0.65
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs10483134; hg19: chr22-27747251;