1-234568520-C-T

Position:

• chr1-234568520-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000429507.1(ENSG00000230404):​n.126-1304C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 151,858 control chromosomes in the GnomAD database, including 6,512 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 0.29 (6512 hom., cov: 31)
• Consequence: ENSG00000230404 ENST00000429507.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972

Genes affected

ENSG00000230404 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985465	XR_001737831.2	n.141+1563G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000230404	ENST00000429507.1	n.126-1304C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43538 AN: 151740 Hom.: 6504 Cov.: 31

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.287 AC: 43576 AN: 151858 Hom.: 6512 Cov.: 31 AF XY: 0.284 AC XY: 21036 AN XY: 74184

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.269

Alfa AF: 0.274 Hom.: 1451

Bravo AF: 0.279

Asia WGS AF: 0.301 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.61
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6703991; hg19: chr1-234704266;