2-220995450-T-C

Variant names:

• chr2-220995450-T-C
• rs1369337
• ENST00000830589.1:n.195+40820A>G

Variant summary

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

The ENST00000830589.1(ENSG00000286272):​n.195+40820A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,128 control chromosomes in the GnomAD database, including 13,729 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 0.40 (13729 hom., cov: 33)
• Consequence: ENSG00000286272 ENST00000830589.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 1 publications found

Genes affected

ENSG00000286272 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830589.1. 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
	ENSG00000286272	ENST00000830589.1		n.195+40820A>G		intron	N/A
	ENSG00000286272	ENST00000830590.1		n.198+40820A>G		intron	N/A
	ENSG00000286272	ENST00000830591.1		n.145+40820A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60083 AN: 152010 Hom.: 13726 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.395 AC: 60103 AN: 152128 Hom.: 13729 Cov.: 33 AF XY: 0.394 AC XY: 29340 AN XY: 74384

African (AFR) AF: 0.165 AC: 6857 AN: 41530

American (AMR) AF: 0.422 AC: 6442 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1602 AN: 3472

East Asian (EAS) AF: 0.334 AC: 1728 AN: 5180

South Asian (SAS) AF: 0.345 AC: 1666 AN: 4826

European-Finnish (FIN) AF: 0.520 AC: 5484 AN: 10554

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34812 AN: 67984

Other (OTH) AF: 0.420 AC: 888 AN: 2114

Alfa AF: 0.480 Hom.: 24454

Bravo AF: 0.381

Asia WGS AF: 0.380 AC: 1321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.76
DANN	Benign	0.40
PhyloP100		-0.091

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1369337;

hg19: chr2-221860170;