chr2-185461222-C-G

Variant names:

• chr2-185461222-C-G
• rs2059357
• ENST00000655441.1:n.540+27031C>G

Variant summary

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

The ENST00000655441.1(ENSG00000286797):​n.540+27031C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,880 control chromosomes in the GnomAD database, including 4,470 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 0.22 (4470 hom., cov: 32)
• Consequence: ENSG00000286797 ENST00000655441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348
• Publications: 3 publications found

Genes affected

ENSG00000286797 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655441.1. 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
	ENSG00000286797	ENST00000655441.1		n.540+27031C>G		intron	N/A
	ENSG00000286797	ENST00000671641.1		n.311-21812C>G		intron	N/A
	ENSG00000286797	ENST00000799165.1		n.253-21812C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33966 AN: 151762 Hom.: 4462 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.224 AC: 33969 AN: 151880 Hom.: 4470 Cov.: 32 AF XY: 0.232 AC XY: 17230 AN XY: 74190

African (AFR) AF: 0.133 AC: 5528 AN: 41448

American (AMR) AF: 0.148 AC: 2259 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 494 AN: 3466

East Asian (EAS) AF: 0.391 AC: 2024 AN: 5170

South Asian (SAS) AF: 0.398 AC: 1919 AN: 4824

European-Finnish (FIN) AF: 0.388 AC: 4086 AN: 10524

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17052 AN: 67908

Other (OTH) AF: 0.202 AC: 426 AN: 2110

Alfa AF: 0.243 Hom.: 657

Bravo AF: 0.196

Asia WGS AF: 0.376 AC: 1302 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.80
DANN	Benign	0.42
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs2059357; hg19: chr2-186325949;