rs1028115

Variant names:

• chr2-16238008-C-T
• rs1028115
• ENST00000420404.2:n.965+8742C>T

Variant summary

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

The ENST00000420404.2(ENSG00000228876):​n.965+8742C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0251 in 152,308 control chromosomes in the GnomAD database, including 282 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 0.025 (282 hom., cov: 33)
• Consequence: ENSG00000228876 ENST00000420404.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 2 publications found

Genes affected

ENSG00000228876 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228876	ENST00000420404.2	n.965+8742C>T		intron_variant	Intron 3 of 3	3
ENSG00000228876	ENST00000642208.1	n.293+8742C>T		intron_variant	Intron 2 of 2
ENSG00000228876	ENST00000644340.1	n.285+8742C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0251 AC: 3825 AN: 152190 Hom.: 282 Cov.: 33

Gnomad AFR AF: 0.00311

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0545

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0123

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00813

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0251 AC: 3824 AN: 152308 Hom.: 282 Cov.: 33 AF XY: 0.0295 AC XY: 2196 AN XY: 74470

African (AFR) AF: 0.00310 AC: 129 AN: 41576

American (AMR) AF: 0.0544 AC: 832 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3470

East Asian (EAS) AF: 0.262 AC: 1355 AN: 5168

South Asian (SAS) AF: 0.142 AC: 685 AN: 4828

European-Finnish (FIN) AF: 0.0123 AC: 131 AN: 10616

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00813 AC: 553 AN: 68040

Other (OTH) AF: 0.0312 AC: 66 AN: 2114

Alfa AF: 0.0168 Hom.: 63

Bravo AF: 0.0275

Asia WGS AF: 0.172 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.9
DANN	Benign	0.68
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs1028115; hg19: chr2-16419276;