rs1011229

Variant names:

• chr2-52825542-T-C
• rs1011229
• ENST00000421575.7:n.239+71701A>G

Variant summary

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

The ENST00000421575.7(ENSG00000228033):​n.239+71701A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0368 in 151,896 control chromosomes in the GnomAD database, including 337 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 0.037 (337 hom., cov: 32)
• Consequence: ENSG00000228033 ENST00000421575.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309
• Publications: 0 publications found

Genes affected

ENSG00000228033 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369165	NR_187747.1	n.171+71701A>G		intron_variant	Intron 3 of 4
LOC105369165	NR_187748.1	n.172-14985A>G		intron_variant	Intron 3 of 6
LOC105369165	NR_187749.1	n.220+71701A>G		intron_variant	Intron 3 of 5
LOC105369165	NR_187750.1	n.172-30686A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228033	ENST00000421575.7	n.239+71701A>G		intron_variant	Intron 3 of 5	5
ENSG00000228033	ENST00000443237.2	n.184+71701A>G		intron_variant	Intron 3 of 4	3
ENSG00000228033	ENST00000668945.1	n.219+71701A>G		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.0367 AC: 5574 AN: 151778 Hom.: 336 Cov.: 32

Gnomad AFR AF: 0.0278

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0168

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.0850

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.00481

Gnomad OTH AF: 0.0508

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

GnomAD4 genome AF: 0.0368 AC: 5583 AN: 151896 Hom.: 337 Cov.: 32 AF XY: 0.0420 AC XY: 3117 AN XY: 74264

African (AFR) AF: 0.0278 AC: 1153 AN: 41506

American (AMR) AF: 0.122 AC: 1861 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.0168 AC: 58 AN: 3454

East Asian (EAS) AF: 0.212 AC: 1091 AN: 5156

South Asian (SAS) AF: 0.0143 AC: 69 AN: 4820

European-Finnish (FIN) AF: 0.0850 AC: 900 AN: 10594

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.00481 AC: 326 AN: 67836

Other (OTH) AF: 0.0502 AC: 106 AN: 2110

Alfa AF: 0.0219 Hom.: 14

Bravo AF: 0.0420

Asia WGS AF: 0.122 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.42
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs1011229; hg19: chr2-53052680;