rs10915864

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723834	XR_426933.4	n.1023+2736A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226349	ENST00000428148.1	n.282-2084T>C		intron_variant	Intron 2 of 2	5
ENSG00000227496	ENST00000448264.2	n.503+12198A>G		intron_variant	Intron 1 of 2	2
ENSG00000227496	ENST00000651661.3	n.909+2736A>G		intron_variant	Intron 2 of 2

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 v4.3

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;