chr2-130013396-A-G

Variant names:

• chr2-130013396-A-G
• rs4233602
• ENST00000444030.5:n.566-1133T>C

Variant summary

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

The ENST00000444030.5(ENSG00000286058):​n.566-1133T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,816 control chromosomes in the GnomAD database, including 22,404 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 0.53 (22404 hom., cov: 32)
• Consequence: ENSG00000286058 ENST00000444030.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 4 publications found

Genes affected

ENSG00000286058 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444030.5. 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
	ENSG00000286058	ENST00000444030.5	TSL:1	n.566-1133T>C		intron	N/A
	ENSG00000286058	ENST00000440931.2	TSL:2	n.283+14913T>C		intron	N/A
	ENSG00000286058	ENST00000715337.1		n.294-1133T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80157 AN: 151698 Hom.: 22399 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.528 AC: 80190 AN: 151816 Hom.: 22404 Cov.: 32 AF XY: 0.529 AC XY: 39216 AN XY: 74186

African (AFR) AF: 0.342 AC: 14112 AN: 41292

American (AMR) AF: 0.668 AC: 10204 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2117 AN: 3472

East Asian (EAS) AF: 0.587 AC: 3029 AN: 5162

South Asian (SAS) AF: 0.550 AC: 2647 AN: 4816

European-Finnish (FIN) AF: 0.537 AC: 5660 AN: 10544

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40589 AN: 67958

Other (OTH) AF: 0.544 AC: 1143 AN: 2102

Alfa AF: 0.447 Hom.: 1349

Bravo AF: 0.530

Asia WGS AF: 0.565 AC: 1966 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.77
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs4233602; hg19: chr2-130770969;