rs11915684

Variant names:

• chr3-127198587-C-T
• rs11915684
• ENST00000654542.1:n.84+19803G>A

Variant summary

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

The ENST00000654542.1(ENSG00000287784):​n.84+19803G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,136 control chromosomes in the GnomAD database, including 1,295 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 0.10 (1295 hom., cov: 32)
• Consequence: ENSG00000287784 ENST00000654542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

Genes affected

ENSG00000287784 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 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
ENSG00000287784	ENST00000654542.1	n.84+19803G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15217 AN: 152018 Hom.: 1300 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0809

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0281

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0394

Gnomad OTH AF: 0.0829

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

GnomAD4 genome AF: 0.100 AC: 15221 AN: 152136 Hom.: 1295 Cov.: 32 AF XY: 0.101 AC XY: 7480 AN XY: 74386

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.0810

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.0281

Gnomad4 NFE AF: 0.0394

Gnomad4 OTH AF: 0.0806

Alfa AF: 0.0671 Hom.: 265

Bravo AF: 0.109

Asia WGS AF: 0.153 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11915684; hg19: chr3-126917430;