rs1822923

chr4-32639002-A-Cchr4-32639002-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, non coding transcript 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: ENST00000659320.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659320.1	n.216-53706T>G		intron_variant, non_coding_transcript_variant

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;