chr22-23950077-T-C

Variant names:

• chr22-23950077-T-C
• rs113413
• ENST00000440099.1:n.88+72T>C

Variant summary

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

The ENST00000703580.1(ENSG00000290199):​n.310-23557A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 706 control chromosomes in the GnomAD database, including 54 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 0.60 (14837 hom., cov: 39)
  • Exomes 𝑓: 0.56 (54 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000290199 ENST00000703580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 17 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=-1.03).
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 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.88+72T>C		intron	N/A
	ENSG00000290199	ENST00000703580.1		n.310-23557A>G		intron	N/A
	ENSG00000290199	ENST00000717616.1		n.136-23557A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.597 AC: 84188 AN: 141026 Hom.: 14798 Cov.: 39

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.549

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.578

GnomAD4 exome AF: 0.561 AC: 396 AN: 706 Hom.: 54 AF XY: 0.574 AC XY: 233 AN XY: 406

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.917 AC: 11 AN: 12

South Asian (SAS) AF: 0.429 AC: 12 AN: 28

European-Finnish (FIN) AF: 0.570 AC: 357 AN: 626

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.393 AC: 11 AN: 28

Other (OTH) AF: 0.400 AC: 4 AN: 10

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.597 AC: 84276 AN: 141128 Hom.: 14837 Cov.: 39 AF XY: 0.594 AC XY: 40935 AN XY: 68924

African (AFR) AF: 0.714 AC: 27163 AN: 38030

American (AMR) AF: 0.551 AC: 7819 AN: 14188

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1836 AN: 3228

East Asian (EAS) AF: 0.639 AC: 2850 AN: 4462

South Asian (SAS) AF: 0.528 AC: 2271 AN: 4302

European-Finnish (FIN) AF: 0.552 AC: 5561 AN: 10082

Middle Eastern (MID) AF: 0.560 AC: 150 AN: 268

European-Non Finnish (NFE) AF: 0.550 AC: 35109 AN: 63806

Other (OTH) AF: 0.580 AC: 1128 AN: 1946

Alfa AF: 0.412 Hom.: 5380

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.1
DANN	Benign	0.52
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs113413; hg19: chr22-24292264;