chr1-159698405-A-G

Variant names:

• chr1-159698405-A-G
• rs2369146
• ENST00000751816.1:n.108-28122A>G

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-28122A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,018 control chromosomes in the GnomAD database, including 41,826 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 0.74 (41826 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 8 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.792 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751816.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297913	ENST00000751816.1		n.108-28122A>G		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.110-28122A>G		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.63-28122A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112063 AN: 151900 Hom.: 41806 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.738 AC: 112128 AN: 152018 Hom.: 41826 Cov.: 32 AF XY: 0.740 AC XY: 54961 AN XY: 74292

African (AFR) AF: 0.619 AC: 25652 AN: 41424

American (AMR) AF: 0.804 AC: 12290 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2868 AN: 3472

East Asian (EAS) AF: 0.813 AC: 4200 AN: 5168

South Asian (SAS) AF: 0.701 AC: 3381 AN: 4822

European-Finnish (FIN) AF: 0.816 AC: 8628 AN: 10572

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52498 AN: 67962

Other (OTH) AF: 0.762 AC: 1604 AN: 2106

Alfa AF: 0.760 Hom.: 139009

Bravo AF: 0.733

Asia WGS AF: 0.725 AC: 2518 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.12
DANN	Benign	0.76
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2369146; hg19: chr1-159668195;