ENST00000833849.1:n.1244+3392A>G

Variant names:

• chr18-21135030-A-G
• rs11873284
• ENST00000833849.1:n.1244+3392A>G

Variant summary

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

The ENST00000833849.1(ENSG00000308413):​n.1244+3392A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,140 control chromosomes in the GnomAD database, including 5,044 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 0.17 (5044 hom., cov: 32)
• Consequence: ENSG00000308413 ENST00000833849.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 7 publications found

Genes affected

ENSG00000308413 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308413	ENST00000833849.1	n.1244+3392A>G		intron_variant	Intron 2 of 2
ENSG00000308413	ENST00000833850.1	n.1172-1079A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26049 AN: 152022 Hom.: 5019 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.0879

Gnomad SAS AF: 0.0342

Gnomad FIN AF: 0.0227

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0350

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.172 AC: 26143 AN: 152140 Hom.: 5044 Cov.: 32 AF XY: 0.168 AC XY: 12532 AN XY: 74376

African (AFR) AF: 0.470 AC: 19483 AN: 41414

American (AMR) AF: 0.183 AC: 2802 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3470

East Asian (EAS) AF: 0.0887 AC: 460 AN: 5188

South Asian (SAS) AF: 0.0346 AC: 167 AN: 4826

European-Finnish (FIN) AF: 0.0227 AC: 241 AN: 10608

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0350 AC: 2380 AN: 68028

Other (OTH) AF: 0.147 AC: 311 AN: 2112

Alfa AF: 0.0753 Hom.: 4558

Bravo AF: 0.199

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.33
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs11873284; hg19: chr18-18714991;