2-59951207-A-G

Variant names:

• chr2-59951207-A-G
• rs890067
• ENST00000606382.1:n.111-123936T>C

Variant summary

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

The ENST00000606382.1(ENSG00000233891):​n.111-123936T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,038 control chromosomes in the GnomAD database, including 30,217 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 0.63 (30217 hom., cov: 33)
• Consequence: ENSG00000233891 ENST00000606382.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 3 publications found

Genes affected

ENSG00000233891 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606382.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233891	ENST00000606382.1	TSL:5	n.111-123936T>C		intron	N/A
	ENSG00000233891	ENST00000650011.1		n.273+44368T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95626 AN: 151920 Hom.: 30171 Cov.: 33

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.630 AC: 95733 AN: 152038 Hom.: 30217 Cov.: 33 AF XY: 0.631 AC XY: 46864 AN XY: 74320

African (AFR) AF: 0.635 AC: 26309 AN: 41432

American (AMR) AF: 0.667 AC: 10194 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1973 AN: 3470

East Asian (EAS) AF: 0.500 AC: 2586 AN: 5176

South Asian (SAS) AF: 0.590 AC: 2840 AN: 4814

European-Finnish (FIN) AF: 0.696 AC: 7365 AN: 10586

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42395 AN: 67972

Other (OTH) AF: 0.607 AC: 1279 AN: 2108

Alfa AF: 0.620 Hom.: 116035

Bravo AF: 0.625

Asia WGS AF: 0.544 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.33
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs890067; hg19: chr2-60178342;