rs10483181

Variant names:

• chr22-34719131-T-C
• rs10483181
• ENST00000440858.1:n.65-5158A>G

Variant summary

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

The ENST00000440858.1(ENSG00000237316):​n.65-5158A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.028 in 152,216 control chromosomes in the GnomAD database, including 92 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 0.028 (92 hom., cov: 33)
• Consequence: ENSG00000237316 ENST00000440858.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531
• Publications: 1 publications found

Genes affected

ENSG00000237316 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440858.1. 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
	ENSG00000237316	ENST00000440858.1	TSL:3	n.65-5158A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0280 AC: 4262 AN: 152098 Hom.: 92 Cov.: 33

Gnomad AFR AF: 0.00899

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0555

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0311

Gnomad FIN AF: 0.0404

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0232

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0280 AC: 4261 AN: 152216 Hom.: 92 Cov.: 33 AF XY: 0.0302 AC XY: 2247 AN XY: 74450

African (AFR) AF: 0.00893 AC: 371 AN: 41524

American (AMR) AF: 0.0556 AC: 850 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0671 AC: 233 AN: 3470

East Asian (EAS) AF: 0.110 AC: 569 AN: 5174

South Asian (SAS) AF: 0.0309 AC: 149 AN: 4824

European-Finnish (FIN) AF: 0.0404 AC: 429 AN: 10618

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0232 AC: 1575 AN: 68004

Other (OTH) AF: 0.0331 AC: 70 AN: 2112

Alfa AF: 0.0235 Hom.: 7

Bravo AF: 0.0286

Asia WGS AF: 0.0580 AC: 201 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.65
PhyloP100		-0.53
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10483181; hg19: chr22-35115122;