chr2-59773585-T-C

Variant names:

• chr2-59773585-T-C
• rs2192512
• ENST00000606382.1:n.236+53561A>G

Variant summary

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

The ENST00000650011.1(ENSG00000233891):​n.514-33364A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,932 control chromosomes in the GnomAD database, including 19,652 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 0.51 (19652 hom., cov: 32)
• Consequence: ENSG00000233891 ENST00000650011.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 5 publications found

Genes affected

ENSG00000233891 (HGNC:58936):

ENSG00000286604 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.572 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.236+53561A>G		intron	N/A
	ENSG00000233891	ENST00000650011.1		n.514-33364A>G		intron	N/A
	ENSG00000286604	ENST00000759172.1		n.169+541T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77051 AN: 151814 Hom.: 19619 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.508 AC: 77124 AN: 151932 Hom.: 19652 Cov.: 32 AF XY: 0.512 AC XY: 38028 AN XY: 74276

African (AFR) AF: 0.499 AC: 20697 AN: 41452

American (AMR) AF: 0.553 AC: 8440 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1820 AN: 3466

East Asian (EAS) AF: 0.571 AC: 2946 AN: 5156

South Asian (SAS) AF: 0.590 AC: 2847 AN: 4824

European-Finnish (FIN) AF: 0.535 AC: 5643 AN: 10550

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33116 AN: 67910

Other (OTH) AF: 0.538 AC: 1136 AN: 2112

Alfa AF: 0.511 Hom.: 3253

Bravo AF: 0.507

Asia WGS AF: 0.601 AC: 2087 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.0
DANN	Benign	0.84
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2192512; hg19: chr2-60000720;