1-230557565-C-G

Position:

• chr1-230557565-C-G

Variant summary

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

The ENST00000685406.1(ENSG00000282564):​n.242-18929C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,346 control chromosomes in the GnomAD database, including 3,575 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 0.21 (3575 hom., cov: 30)
• Consequence: ENSG00000282564 ENST00000685406.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224

Genes affected

ENSG00000282564 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985357	XR_007066934.1	n.171-1204G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000282564	ENST00000685406.1	n.242-18929C>G		intron_variant
ENSG00000282564	ENST00000689608.1	n.329+58599C>G		intron_variant
ENSG00000282564	ENST00000692577.2	n.318+58599C>G		intron_variant
ENSG00000282564	ENST00000702785.1	n.264-22189C>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31584 AN: 151230 Hom.: 3573 Cov.: 30

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.209 AC: 31599 AN: 151346 Hom.: 3575 Cov.: 30 AF XY: 0.209 AC XY: 15422 AN XY: 73898

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.225

Alfa AF: 0.215 Hom.: 430

Bravo AF: 0.204

Asia WGS AF: 0.383 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1752189; hg19: chr1-230693311;