rs10768682

chr11-5224277-G-A

Variant summary

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

The 11-5224277-G-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,046 control chromosomes in the GnomAD database, including 49,761 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 0.80 (49761 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENST00000644706.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

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 (AFR) allele frequency at 95% confidence interval = 0.848 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
	ENST00000644706.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122254 AN: 151928 Hom.: 49728 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.816

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.805 AC: 122340 AN: 152046 Hom.: 49761 Cov.: 32 AF XY: 0.796 AC XY: 59197 AN XY: 74332

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.849

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.813

Alfa AF: 0.818 Hom.: 6585

Bravo AF: 0.809

Asia WGS AF: 0.565 AC: 1959 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.3
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10768682; hg19: chr11-5245507;