ENST00000426321.2:n.391+1929A>G

Variant names:

• chr1-111321905-T-C
• rs12034177
• ENST00000426321.2:n.391+1929A>G

Variant summary

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

The ENST00000426321.2(ENSG00000229283):​n.391+1929A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,160 control chromosomes in the GnomAD database, including 5,447 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 0.25 (5447 hom., cov: 32)
• Consequence: ENSG00000229283 ENST00000426321.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 5 publications found

Genes affected

ENSG00000229283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.359 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
ENSG00000229283	ENST00000426321.2	n.391+1929A>G		intron_variant	Intron 3 of 3	3
ENSG00000229283	ENST00000725074.1	n.369+1929A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38213 AN: 152042 Hom.: 5450 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.251 AC: 38208 AN: 152160 Hom.: 5447 Cov.: 32 AF XY: 0.253 AC XY: 18812 AN XY: 74368

African (AFR) AF: 0.128 AC: 5335 AN: 41526

American (AMR) AF: 0.193 AC: 2959 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1159 AN: 3464

East Asian (EAS) AF: 0.341 AC: 1768 AN: 5188

South Asian (SAS) AF: 0.373 AC: 1801 AN: 4822

European-Finnish (FIN) AF: 0.320 AC: 3378 AN: 10558

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.307 AC: 20862 AN: 67990

Other (OTH) AF: 0.245 AC: 517 AN: 2114

Alfa AF: 0.298 Hom.: 3640

Bravo AF: 0.233

Asia WGS AF: 0.316 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.6
DANN	Benign	0.65
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs12034177; hg19: chr1-111864527;