rs1120038

Variant names:

• chr15-46565724-A-G
• rs1120038
• ENST00000661853.1:n.46-94491A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661853.1(ENSG00000287704):​n.46-94491A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 151,850 control chromosomes in the GnomAD database, including 7,562 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 0.31 (7562 hom., cov: 31)
• Consequence: ENSG00000287704 ENST00000661853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

ENSG00000287704 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.355 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
ENSG00000287704	ENST00000661853.1	n.46-94491A>G		intron_variant	Intron 1 of 1
ENSG00000287704	ENST00000686120.1	n.57-12483A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47276 AN: 151732 Hom.: 7558 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.311 AC: 47297 AN: 151850 Hom.: 7562 Cov.: 31 AF XY: 0.309 AC XY: 22925 AN XY: 74208

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.376

Alfa AF: 0.328 Hom.: 1024

Bravo AF: 0.317

Asia WGS AF: 0.199 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.88
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1120038; hg19: chr15-46857922;