22-27277250-C-T

Variant names:

• chr22-27277250-C-T
• rs134806
• ENST00000449126.1:n.105+906C>T

Variant summary

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

The ENST00000449126.1(ENSG00000233574):​n.105+906C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,120 control chromosomes in the GnomAD database, including 5,380 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 0.24 (5380 hom., cov: 32)
• Consequence: ENSG00000233574 ENST00000449126.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495
• Publications: 1 publications found

Genes affected

ENSG00000233574 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449126.1. 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
	ENSG00000233574	ENST00000449126.1	TSL:3	n.105+906C>T		intron	N/A
	ENSG00000233574	ENST00000783519.1		n.133+906C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37130 AN: 151998 Hom.: 5364 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.0983

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.245 AC: 37199 AN: 152120 Hom.: 5380 Cov.: 32 AF XY: 0.248 AC XY: 18421 AN XY: 74366

African (AFR) AF: 0.392 AC: 16246 AN: 41480

American (AMR) AF: 0.294 AC: 4487 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0983 AC: 341 AN: 3470

East Asian (EAS) AF: 0.104 AC: 539 AN: 5178

South Asian (SAS) AF: 0.258 AC: 1240 AN: 4814

European-Finnish (FIN) AF: 0.251 AC: 2663 AN: 10592

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11176 AN: 67992

Other (OTH) AF: 0.210 AC: 442 AN: 2108

Alfa AF: 0.174 Hom.: 1676

Bravo AF: 0.256

Asia WGS AF: 0.203 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.51
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs134806; hg19: chr22-27673211;