18-77217086-G-A

Position:

• chr18-77217086-G-A

Variant summary

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

The ENST00000584843.1(ENSG00000265844):​n.330+11527G>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 0.407 in 152,084 control chromosomes in the GnomAD database, including 13,248 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 0.41 (13248 hom., cov: 34)
• Consequence: ENST00000584843.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000584843.1	n.330+11527G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61799 AN: 151966 Hom.: 13239 Cov.: 34

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.407 AC: 61827 AN: 152084 Hom.: 13248 Cov.: 34 AF XY: 0.410 AC XY: 30447 AN XY: 74342

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.731

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.385

Alfa AF: 0.418 Hom.: 7362

Bravo AF: 0.403

Asia WGS AF: 0.527 AC: 1832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2717096; hg19: chr18-74929042;