rs1120038

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

ENSG00000287704 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661853.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287704	ENST00000661853.1		n.46-94491A>G		intron	N/A
	ENSG00000287704	ENST00000686120.1		n.57-12483A>G		intron	N/A
	ENSG00000287704	ENST00000736459.1		n.47-12483A>G		intron	N/A

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

African (AFR) AF: 0.232 AC: 9634 AN: 41444

American (AMR) AF: 0.363 AC: 5534 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1278 AN: 3468

East Asian (EAS) AF: 0.159 AC: 817 AN: 5136

South Asian (SAS) AF: 0.218 AC: 1050 AN: 4810

European-Finnish (FIN) AF: 0.315 AC: 3321 AN: 10546

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24269 AN: 67880

Other (OTH) AF: 0.376 AC: 793 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.88
DANN	Benign	0.75
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1120038; hg19: chr15-46857922;