rs1317019

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373456	XR_007086234.1	n.1138+39891A>G		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287284	ENST00000776740.1	n.364+15366A>G		intron_variant	Intron 3 of 4
ENSG00000287284	ENST00000776741.1	n.321+15366A>G		intron_variant	Intron 3 of 3

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 v4.3

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;