rs12473113

chr2-60033155-G-A

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, non coding transcript 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: ENST00000606382.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000606382.1	n.110+66936C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000650011.1	n.213-37520C>T		intron_variant, non_coding_transcript_variant

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;