rs1219414

chr11-121927189-G-Achr11-121927189-G-T

Variant summary

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

The ENST00000652518.1(ENSG00000286044):n.1879-177G>A 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 0.309 in 152,028 control chromosomes in the GnomAD database, including 7,530 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 (7530 hom., cov: 32)
• Consequence: ENST00000652518.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 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
	ENST00000652518.1	n.1879-177G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46961 AN: 151910 Hom.: 7514 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.0714

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.309 AC: 46991 AN: 152028 Hom.: 7530 Cov.: 32 AF XY: 0.307 AC XY: 22779 AN XY: 74306

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.0710

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.330

Alfa AF: 0.329 Hom.: 11067

Bravo AF: 0.303

Asia WGS AF: 0.151 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.54
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1219414; hg19: chr11-121797897;