chr1-159357090-A-G

Position:

• chr1-159357090-A-G

Variant summary

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

The ENST00000431862.1(ENSG00000228560):​n.539+4684T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 151,868 control chromosomes in the GnomAD database, including 2,022 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 0.14 (2022 hom., cov: 32)
• Consequence: ENSG00000228560 ENST00000431862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

Genes affected

ENSG00000228560 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904433	XR_007066672.1	n.186+7234T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000228560	ENST00000431862.1	n.539+4684T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21499 AN: 151750 Hom.: 2022 Cov.: 32

Gnomad AFR AF: 0.0369

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.142 AC: 21494 AN: 151868 Hom.: 2022 Cov.: 32 AF XY: 0.140 AC XY: 10387 AN XY: 74224

Gnomad4 AFR AF: 0.0368

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.158

Alfa AF: 0.188 Hom.: 1010

Bravo AF: 0.131

Asia WGS AF: 0.0440 AC: 153 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4656784; hg19: chr1-159326880;