2-18959268-A-G

Variant names:

• chr2-18959268-A-G
• rs1317019
• ENST00000776740.1:n.364+15366A>G

Variant summary

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

The ENST00000776740.1(ENSG00000287284):​n.364+15366A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 151,972 control chromosomes in the GnomAD database, including 5,918 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 (5918 hom., cov: 32)
• Consequence: ENSG00000287284 ENST00000776740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 3 publications found

Genes affected

ENSG00000287284 (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 = 0.437 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776740.1. 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
	ENSG00000287284	ENST00000776740.1		n.364+15366A>G		intron	N/A
	ENSG00000287284	ENST00000776741.1		n.321+15366A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41068 AN: 151854 Hom.: 5891 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.271 AC: 41144 AN: 151972 Hom.: 5918 Cov.: 32 AF XY: 0.270 AC XY: 20063 AN XY: 74294

African (AFR) AF: 0.327 AC: 13547 AN: 41446

American (AMR) AF: 0.283 AC: 4317 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1208 AN: 3464

East Asian (EAS) AF: 0.452 AC: 2333 AN: 5160

South Asian (SAS) AF: 0.327 AC: 1576 AN: 4824

European-Finnish (FIN) AF: 0.187 AC: 1985 AN: 10588

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.225 AC: 15313 AN: 67932

Other (OTH) AF: 0.294 AC: 618 AN: 2102

Alfa AF: 0.236 Hom.: 7422

Bravo AF: 0.278

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.011
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1317019; hg19: chr2-19140546;