rs2014838

Variant names:

• chr22-24694039-A-G
• rs2014838
• ENST00000633827.3:n.187+1808T>C

Variant summary

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

The ENST00000633827.3(ENSG00000282012):​n.187+1808T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 152,062 control chromosomes in the GnomAD database, including 27,852 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 (27852 hom., cov: 33)
• Consequence: ENSG00000282012 ENST00000633827.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 2 publications found

Genes affected

ENSG00000282012 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000633827.3. 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
	ENSG00000282012	ENST00000633827.3	TSL:2	n.187+1808T>C		intron	N/A
	ENSG00000282012	ENST00000748010.1		n.158+1808T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90982 AN: 151944 Hom.: 27811 Cov.: 33

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.599 AC: 91077 AN: 152062 Hom.: 27852 Cov.: 33 AF XY: 0.598 AC XY: 44450 AN XY: 74324

African (AFR) AF: 0.734 AC: 30484 AN: 41506

American (AMR) AF: 0.594 AC: 9077 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1730 AN: 3464

East Asian (EAS) AF: 0.576 AC: 2983 AN: 5178

South Asian (SAS) AF: 0.682 AC: 3285 AN: 4814

European-Finnish (FIN) AF: 0.507 AC: 5362 AN: 10574

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36162 AN: 67938

Other (OTH) AF: 0.583 AC: 1230 AN: 2110

Alfa AF: 0.558 Hom.: 9178

Bravo AF: 0.609

Asia WGS AF: 0.638 AC: 2219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.9
DANN	Benign	0.25
PhyloP100		-1.2

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: rs2014838;

hg19: chr22-25090006;