rs2330649

Variant names:

• chr22-23952866-G-A
• rs2330649
• ENST00000440099.1:n.133+648G>A

Your query was ambiguous. Multiple possible variants found:

• chr22-23952866-G-A
• chr22-23952866-G-C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000703580.1(ENSG00000290199):​n.309+20902C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.36 (522 hom., cov: 46)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000290199 ENST00000703580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.667
• Publications: 7 publications found

Genes affected

ENSG00000231271 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000703580.1. 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
	ENSG00000231271	ENST00000440099.1	TSL:6	n.133+648G>A		intron	N/A
	ENSG00000290199	ENST00000703580.1		n.309+20902C>T		intron	N/A
	ENSG00000290199	ENST00000717616.1		n.135+21441C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.359 AC: 52010 AN: 144994 Hom.: 520 Cov.: 46

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.352

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.370

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.359 AC: 52032 AN: 145108 Hom.: 522 Cov.: 46 AF XY: 0.362 AC XY: 25600 AN XY: 70754

African (AFR) AF: 0.245 AC: 9399 AN: 38438

American (AMR) AF: 0.374 AC: 5407 AN: 14450

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1312 AN: 3346

East Asian (EAS) AF: 0.245 AC: 1180 AN: 4808

South Asian (SAS) AF: 0.461 AC: 2131 AN: 4622

European-Finnish (FIN) AF: 0.416 AC: 4266 AN: 10260

Middle Eastern (MID) AF: 0.348 AC: 96 AN: 276

European-Non Finnish (NFE) AF: 0.410 AC: 27099 AN: 66032

Other (OTH) AF: 0.368 AC: 734 AN: 1992

Alfa AF: 0.442 Hom.: 1133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.70
PhyloP100		0.67

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: rs2330649;

hg19: chr22-24295053;