ENST00000814154.1:n.90+962C>G

Variant names:

• chr2-96747751-C-G
• rs2314398
• ENST00000814154.1:n.90+962C>G

Variant summary

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

The ENST00000814154.1(ENSG00000305927):​n.90+962C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,008 control chromosomes in the GnomAD database, including 6,052 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 0.27 (6052 hom., cov: 32)
• Consequence: ENSG00000305927 ENST00000814154.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.635
• Publications: 28 publications found

Genes affected

ENSG00000305927 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000814154.1. 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
	ENSG00000305927	ENST00000814154.1		n.90+962C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40787 AN: 151888 Hom.: 6058 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.268 AC: 40793 AN: 152008 Hom.: 6052 Cov.: 32 AF XY: 0.272 AC XY: 20174 AN XY: 74304

African (AFR) AF: 0.187 AC: 7754 AN: 41476

American (AMR) AF: 0.200 AC: 3053 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 743 AN: 3468

East Asian (EAS) AF: 0.321 AC: 1658 AN: 5166

South Asian (SAS) AF: 0.184 AC: 886 AN: 4824

European-Finnish (FIN) AF: 0.447 AC: 4707 AN: 10536

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21266 AN: 67950

Other (OTH) AF: 0.220 AC: 465 AN: 2116

Alfa AF: 0.297 Hom.: 3922

Bravo AF: 0.250

Asia WGS AF: 0.261 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.8
DANN	Benign	0.51
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs2314398; hg19: chr2-97413488;