rs2189829

Variant names:

• chr7-49570267-G-C
• rs2189829
• ENST00000664348.2:n.224-14056G>C

Variant summary

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

The ENST00000664348.2(ENSG00000286995):​n.224-14056G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,090 control chromosomes in the GnomAD database, including 3,318 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 0.20 (3318 hom., cov: 32)
• Consequence: ENSG00000286995 ENST00000664348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 1 publications found

Genes affected

ENSG00000286995 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664348.2. 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
	ENSG00000286995	ENST00000664348.2		n.224-14056G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30150 AN: 151972 Hom.: 3311 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.198 AC: 30185 AN: 152090 Hom.: 3318 Cov.: 32 AF XY: 0.201 AC XY: 14940 AN XY: 74354

African (AFR) AF: 0.130 AC: 5411 AN: 41514

American (AMR) AF: 0.141 AC: 2158 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 548 AN: 3470

East Asian (EAS) AF: 0.305 AC: 1576 AN: 5168

South Asian (SAS) AF: 0.298 AC: 1436 AN: 4824

European-Finnish (FIN) AF: 0.281 AC: 2964 AN: 10530

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15545 AN: 67974

Other (OTH) AF: 0.187 AC: 395 AN: 2114

Alfa AF: 0.221 Hom.: 479

Bravo AF: 0.182

Asia WGS AF: 0.268 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.29
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs2189829; hg19: chr7-49609863;