1-229231368-T-C

Variant names:

• chr1-229231368-T-C
• rs342818
• ENST00000651412.1:n.253-3603A>G

Variant summary

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

The ENST00000651412.1(ENSG00000233920):​n.253-3603A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,052 control chromosomes in the GnomAD database, including 10,272 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 0.36 (10272 hom., cov: 32)
• Consequence: ENSG00000233920 ENST00000651412.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948

Genes affected

ENSG00000233920 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 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
ENSG00000233920	ENST00000651412.1	n.253-3603A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53943 AN: 151934 Hom.: 10252 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.355 AC: 54012 AN: 152052 Hom.: 10272 Cov.: 32 AF XY: 0.354 AC XY: 26311 AN XY: 74314

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.320

Alfa AF: 0.311 Hom.: 15791

Bravo AF: 0.357

Asia WGS AF: 0.267 AC: 927 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	5.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs342818; hg19: chr1-229367115;