rs12473113

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000606382.1(ENSG00000271955):​n.110+66936C>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: ENSG00000271955 ENST00000606382.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

Genes affected

ENSG00000271955 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000271955	ENST00000606382.1	n.110+66936C>T		intron_variant	Intron 1 of 3	5
ENSG00000271955	ENST00000650011.1	n.213-37520C>T		intron_variant	Intron 1 of 5

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

Gnomad4 AFR AF: 0.0211

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.0622

Gnomad4 NFE AF: 0.0831

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.0818 Hom.: 66

Bravo AF: 0.0824

Asia WGS AF: 0.158 AC: 549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12473113; hg19: chr2-60260290;