rs1120038

Positions:

• chr15-46565724-A-G

Variant summary

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

The ENST00000686120.1(ENSG00000287704):​n.57-12483A>G variant causes a intron, non coding transcript 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: ENST00000686120.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000686120.1	n.57-12483A>G		intron_variant, non_coding_transcript_variant
	ENST00000661853.1	n.46-94491A>G		intron_variant, non_coding_transcript_variant

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;