2-60054473-G-C

Variant names:

• chr2-60054473-G-C
• rs6712720
• ENST00000606382.1:n.110+45618C>G

Variant summary

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

The ENST00000650011.1(ENSG00000233891):​n.212+21996C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 152,034 control chromosomes in the GnomAD database, including 22,646 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 0.54 (22646 hom., cov: 32)
• Consequence: ENSG00000233891 ENST00000650011.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.702
• Publications: 8 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 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+45618C>G		intron	N/A
	ENSG00000233891	ENST00000650011.1		n.212+21996C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81669 AN: 151916 Hom.: 22618 Cov.: 32

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.538 AC: 81758 AN: 152034 Hom.: 22646 Cov.: 32 AF XY: 0.534 AC XY: 39689 AN XY: 74300

African (AFR) AF: 0.653 AC: 27063 AN: 41452

American (AMR) AF: 0.452 AC: 6904 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1589 AN: 3470

East Asian (EAS) AF: 0.330 AC: 1708 AN: 5168

South Asian (SAS) AF: 0.403 AC: 1941 AN: 4822

European-Finnish (FIN) AF: 0.638 AC: 6742 AN: 10566

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34227 AN: 67966

Other (OTH) AF: 0.469 AC: 989 AN: 2108

Alfa AF: 0.483 Hom.: 9282

Bravo AF: 0.528

Asia WGS AF: 0.399 AC: 1388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.38
DANN	Benign	0.55
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs6712720; hg19: chr2-60281608;