1-225713304-A-G

Variant names:

• chr1-225713304-A-G
• rs10915864
• ENST00000428148.1:n.282-2084T>C

Variant summary

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

The ENST00000428148.1(ENSG00000226349):​n.282-2084T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,090 control chromosomes in the GnomAD database, including 3,313 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 (3313 hom., cov: 31)
• Consequence: ENSG00000226349 ENST00000428148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425
• Publications: 8 publications found

Genes affected

ENSG00000226349 (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 = 0.252 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428148.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226349	ENST00000428148.1	TSL:5	n.282-2084T>C		intron	N/A
	ENSG00000227496	ENST00000448264.2	TSL:2	n.503+12198A>G		intron	N/A
	ENSG00000227496	ENST00000651661.3		n.909+2736A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31511 AN: 151972 Hom.: 3313 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.207 AC: 31538 AN: 152090 Hom.: 3313 Cov.: 31 AF XY: 0.207 AC XY: 15416 AN XY: 74338

African (AFR) AF: 0.191 AC: 7924 AN: 41478

American (AMR) AF: 0.256 AC: 3916 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 804 AN: 3470

East Asian (EAS) AF: 0.263 AC: 1360 AN: 5168

South Asian (SAS) AF: 0.170 AC: 819 AN: 4816

European-Finnish (FIN) AF: 0.190 AC: 2008 AN: 10582

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13962 AN: 67982

Other (OTH) AF: 0.227 AC: 479 AN: 2114

Alfa AF: 0.209 Hom.: 10804

Bravo AF: 0.210

Asia WGS AF: 0.242 AC: 842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.69
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10915864; hg19: chr1-225901006;