rs12473113

Variant names:

• chr2-60033155-G-A
• rs12473113
• ENST00000606382.1:n.110+66936C>T

Variant summary

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

The ENST00000650011.1(ENSG00000233891):​n.213-37520C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0803 in 152,236 control chromosomes in the GnomAD database, including 732 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 0.080 (732 hom., cov: 32)
• Consequence: ENSG00000233891 ENST00000650011.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160
• Publications: 2 publications found

Genes affected

ENSG00000233891 (HGNC:58936):

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 = 0.199 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650011.1. 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
	ENSG00000233891	ENST00000606382.1	TSL:5	n.110+66936C>T		intron	N/A
	ENSG00000233891	ENST00000650011.1		n.213-37520C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0803 AC: 12218 AN: 152118 Hom.: 731 Cov.: 32

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.0622

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0831

Gnomad OTH AF: 0.0828

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

GnomAD4 genome AF: 0.0803 AC: 12232 AN: 152236 Hom.: 732 Cov.: 32 AF XY: 0.0853 AC XY: 6346 AN XY: 74424

African (AFR) AF: 0.0211 AC: 875 AN: 41558

American (AMR) AF: 0.158 AC: 2412 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3470

East Asian (EAS) AF: 0.209 AC: 1083 AN: 5178

South Asian (SAS) AF: 0.195 AC: 939 AN: 4820

European-Finnish (FIN) AF: 0.0622 AC: 659 AN: 10598

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.0831 AC: 5649 AN: 68002

Other (OTH) AF: 0.0829 AC: 175 AN: 2112

Alfa AF: 0.0791 Hom.: 66

Bravo AF: 0.0824

Asia WGS AF: 0.158 AC: 549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.4
DANN	Benign	0.69
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs12473113; hg19: chr2-60260290;