22-23947178-T-C

Variant names:

• chr22-23947178-T-C
• rs575959
• ENST00000703580.1:n.310-20658A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000703580.1(ENSG00000290199):​n.310-20658A>G variant causes a intron 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 0.0000097 (0 hom., cov: 17)
• Consequence: ENSG00000290199 ENST00000703580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 7 publications found

Genes affected

ENSG00000290199 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).

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
ENSG00000290199	ENST00000703580.1	n.310-20658A>G		intron_variant	Intron 2 of 3
ENSG00000290199	ENST00000717616.1	n.136-20658A>G		intron_variant	Intron 1 of 2
ENSG00000290199	ENST00000717617.1	n.136-20658A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.00000971 AC: 1 AN: 102998 Hom.: 0 Cov.: 17

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000209

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000971 AC: 1 AN: 102998 Hom.: 0 Cov.: 17 AF XY: 0.00 AC XY: 0 AN XY: 49106

African (AFR) AF: 0.00 AC: 0 AN: 28812

American (AMR) AF: 0.00 AC: 0 AN: 9636

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2504

East Asian (EAS) AF: 0.00 AC: 0 AN: 3776

South Asian (SAS) AF: 0.00 AC: 0 AN: 2444

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5872

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 230

European-Non Finnish (NFE) AF: 0.0000209 AC: 1 AN: 47876

Other (OTH) AF: 0.00 AC: 0 AN: 1336

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.20
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs575959; hg19: chr22-24289365;