rs1822923

Variant names:

• chr4-32639002-A-C
• rs1822923
• ENST00000659320.1:n.216-53706T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-32639002-A-C
• chr4-32639002-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659320.1(ENSG00000286784):​n.216-53706T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,102 control chromosomes in the GnomAD database, including 45,105 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 0.76 (45105 hom., cov: 32)
• Consequence: ENSG00000286784 ENST00000659320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

Genes affected

ENSG00000286784 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286784	ENST00000659320.1	n.216-53706T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116143 AN: 151984 Hom.: 45059 Cov.: 32

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.764 AC: 116245 AN: 152102 Hom.: 45105 Cov.: 32 AF XY: 0.763 AC XY: 56677 AN XY: 74314

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.750

Alfa AF: 0.721 Hom.: 38731

Bravo AF: 0.784

Asia WGS AF: 0.895 AC: 3109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1822923; hg19: chr4-32640624;