chr22-27533892-T-C

Variant names:

• chr22-27533892-T-C
• rs926937
• ENST00000761705.1:n.255-24947A>G

Variant summary

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

The ENST00000761705.1(ENSG00000224027):​n.255-24947A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,206 control chromosomes in the GnomAD database, including 60,713 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 0.89 (60713 hom., cov: 31)
• Consequence: ENSG00000224027 ENST00000761705.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 3 publications found

Genes affected

ENSG00000224027 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761705.1. 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
	ENSG00000224027	ENST00000761705.1		n.255-24947A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135225 AN: 152088 Hom.: 60690 Cov.: 31

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.943

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.904

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

GnomAD4 genome AF: 0.889 AC: 135299 AN: 152206 Hom.: 60713 Cov.: 31 AF XY: 0.892 AC XY: 66366 AN XY: 74414

African (AFR) AF: 0.756 AC: 31402 AN: 41512

American (AMR) AF: 0.920 AC: 14067 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.938 AC: 3257 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5153 AN: 5158

South Asian (SAS) AF: 0.943 AC: 4532 AN: 4808

European-Finnish (FIN) AF: 0.980 AC: 10408 AN: 10620

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.933 AC: 63451 AN: 68022

Other (OTH) AF: 0.903 AC: 1911 AN: 2116

Alfa AF: 0.932 Hom.: 132298

Bravo AF: 0.878

Asia WGS AF: 0.957 AC: 3329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	9.2
DANN	Benign	0.81
PhyloP100		0.22

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs926937;

hg19: chr22-27929853;