chr22-23953099-T-C

Variant names:

• chr22-23953099-T-C
• rs2739330
• ENST00000440099.1:n.134-788T>C

Variant summary

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

The ENST00000703580.1(ENSG00000290199):​n.309+20669A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 147,752 control chromosomes in the GnomAD database, including 23,139 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 0.58 (23139 hom., cov: 44)
• Consequence: ENSG00000290199 ENST00000703580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 34 publications found

Genes affected

ENSG00000231271 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000703580.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231271	ENST00000440099.1	TSL:6	n.134-788T>C		intron	N/A
	ENSG00000290199	ENST00000703580.1		n.309+20669A>G		intron	N/A
	ENSG00000290199	ENST00000717616.1		n.135+21208A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.576 AC: 85049 AN: 147638 Hom.: 23116 Cov.: 44

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.576 AC: 85113 AN: 147752 Hom.: 23139 Cov.: 44 AF XY: 0.581 AC XY: 41902 AN XY: 72124

African (AFR) AF: 0.508 AC: 19587 AN: 38578

American (AMR) AF: 0.603 AC: 8985 AN: 14900

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1911 AN: 3442

East Asian (EAS) AF: 0.411 AC: 1954 AN: 4756

South Asian (SAS) AF: 0.692 AC: 3272 AN: 4730

European-Finnish (FIN) AF: 0.635 AC: 6684 AN: 10524

Middle Eastern (MID) AF: 0.599 AC: 170 AN: 284

European-Non Finnish (NFE) AF: 0.602 AC: 40685 AN: 67574

Other (OTH) AF: 0.578 AC: 1192 AN: 2064

Alfa AF: 0.582 Hom.: 2751

Asia WGS AF: 0.505 AC: 1688 AN: 3346

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.42
PhyloP100		-0.0060

Splicing

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

Other links and lift over

dbSNP: rs2739330; hg19: chr22-24295286;