9-22956520-T-C

Variant names:

• chr9-22956520-T-C
• rs1599698
• ENST00000640003.1:n.368+49560A>G

Variant summary

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

The ENST00000640003.1(ENSG00000284418):​n.368+49560A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.925 in 152,256 control chromosomes in the GnomAD database, including 65,204 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 0.92 (65204 hom., cov: 32)
• Consequence: ENSG00000284418 ENST00000640003.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759

Genes affected

ENSG00000284418 (HGNC:58153):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.935 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
ENSG00000284418	ENST00000640003.1	n.368+49560A>G		intron_variant	Intron 3 of 9	5

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140755 AN: 152138 Hom.: 65184 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.945

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.935

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.925 AC: 140828 AN: 152256 Hom.: 65204 Cov.: 32 AF XY: 0.925 AC XY: 68877 AN XY: 74438

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.913

Gnomad4 ASJ AF: 0.917

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.945

Gnomad4 FIN AF: 0.968

Gnomad4 NFE AF: 0.936

Gnomad4 OTH AF: 0.917

Alfa AF: 0.928 Hom.: 62554

Bravo AF: 0.921

Asia WGS AF: 0.905 AC: 3145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
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: rs1599698; hg19: chr9-22956519;