rs2330649

Positions:

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

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000440099.1(ENSG00000231271):​n.133+648G>A variant causes a intron, non coding transcript 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: ENST00000440099.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.667

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000440099.1	n.133+648G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 52010 AN: 144994 Hom.: 520 Cov.: 46 FAILED QC

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

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.368

Alfa AF: 0.442 Hom.: 1133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2330649; hg19: chr22-24295053;