rs10203166

Variant names:

• chr2-59562570-C-T
• rs10203166
• ENST00000412409.3:n.545+32235G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000412409.3(ENSG00000233891):​n.545+32235G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0525 in 152,242 control chromosomes in the GnomAD database, including 361 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 0.052 (361 hom., cov: 32)
• Consequence: ENSG00000233891 ENST00000412409.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 4 publications found

Genes affected

ENSG00000233891 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000233891	ENST00000412409.3	n.545+32235G>A		intron_variant	Intron 4 of 4	3
ENSG00000233891	ENST00000606382.1	n.237-50365G>A		intron_variant	Intron 2 of 3	5
ENSG00000233891	ENST00000717264.1	n.262-3135G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.0524 AC: 7967 AN: 152124 Hom.: 356 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0336

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00828

Gnomad FIN AF: 0.0287

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0283

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0525 AC: 7990 AN: 152242 Hom.: 361 Cov.: 32 AF XY: 0.0516 AC XY: 3840 AN XY: 74438

African (AFR) AF: 0.118 AC: 4909 AN: 41530

American (AMR) AF: 0.0335 AC: 513 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0352 AC: 122 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00849 AC: 41 AN: 4828

European-Finnish (FIN) AF: 0.0287 AC: 304 AN: 10608

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0283 AC: 1925 AN: 68018

Other (OTH) AF: 0.0488 AC: 103 AN: 2110

Alfa AF: 0.0536 Hom.: 236

Bravo AF: 0.0545

Asia WGS AF: 0.0150 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	12
DANN	Benign	0.59
PhyloP100		0.32
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: rs10203166; hg19: chr2-59789705;