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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124905092	XR_007068025.1	n.187+1808T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282012	ENST00000633827.3	n.187+1808T>C		intron_variant	Intron 1 of 1	2
ENSG00000282012	ENST00000748010.1	n.158+1808T>C		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs2014838; hg19: chr22-25090006;