22-23956960-C-T

Variant names:

• chr22-23956960-C-T
• rs5742303
• ENST00000703580.1:n.309+16808G>A

Variant summary

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

The ENST00000703580.1(ENSG00000290199):​n.309+16808G>A 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 0.52 (18071 hom., cov: 17)
• Consequence: ENSG00000290199 ENST00000703580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 12 publications found

Genes affected

ENSG00000290199 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.648 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
ENSG00000290199	ENST00000703580.1	n.309+16808G>A		intron_variant	Intron 2 of 3
ENSG00000290199	ENST00000717616.1	n.135+17347G>A		intron_variant	Intron 1 of 2
ENSG00000290199	ENST00000717617.1	n.135+17347G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.518 AC: 64898 AN: 125312 Hom.: 18063 Cov.: 17

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.514

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.518 AC: 64918 AN: 125386 Hom.: 18071 Cov.: 17 AF XY: 0.522 AC XY: 31324 AN XY: 59996

African (AFR) AF: 0.357 AC: 9717 AN: 27242

American (AMR) AF: 0.529 AC: 6744 AN: 12760

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1696 AN: 3200

East Asian (EAS) AF: 0.312 AC: 1183 AN: 3786

South Asian (SAS) AF: 0.670 AC: 2546 AN: 3800

European-Finnish (FIN) AF: 0.597 AC: 5251 AN: 8800

Middle Eastern (MID) AF: 0.512 AC: 133 AN: 260

European-Non Finnish (NFE) AF: 0.574 AC: 36171 AN: 62968

Other (OTH) AF: 0.509 AC: 877 AN: 1724

Alfa AF: 0.538 Hom.: 2603

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.69
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs5742303; hg19: chr22-24299147;