chr9-22956520-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000764217.1(ENSG00000284418):​n.118+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 ENST00000764217.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759
• Publications: 0 publications found

Genes affected

ENSG00000284418 (HGNC:58153):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000764217.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000284418	ENST00000640003.1	TSL:5	n.368+49560A>G		intron	N/A
	ENSG00000284418	ENST00000764217.1		n.118+49560A>G		intron	N/A
	ENSG00000284418	ENST00000764218.1		n.118+49560A>G		intron	N/A

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

African (AFR) AF: 0.896 AC: 37219 AN: 41546

American (AMR) AF: 0.913 AC: 13958 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 3182 AN: 3470

East Asian (EAS) AF: 0.957 AC: 4945 AN: 5166

South Asian (SAS) AF: 0.945 AC: 4561 AN: 4828

European-Finnish (FIN) AF: 0.968 AC: 10278 AN: 10614

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.936 AC: 63647 AN: 68034

Other (OTH) AF: 0.917 AC: 1937 AN: 2112

Alfa AF: 0.927 Hom.: 81921

Bravo AF: 0.921

Asia WGS AF: 0.905 AC: 3145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.34
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs1599698; hg19: chr9-22956519;