rs2468680

Positions:

• chr8-139508977-G-A
• chr8-139508977-G-C
• chr8-139508977-G-T

Variant summary

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

The 8-139508977-G-A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,116 control chromosomes in the GnomAD database, including 6,966 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 0.29 (6963 hom., cov: 33)
  • Exomes 𝑓: 0.38 (3 hom.)
• Consequence: ENST00000611315.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 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
	ENST00000611315.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44109 AN: 151974 Hom.: 6956 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.308

GnomAD4 exome AF: 0.375 AC: 9 AN: 24 Hom.: 3 Cov.: 0 AF XY: 0.563 AC XY: 9 AN XY: 16

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.400

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.290 AC: 44141 AN: 152092 Hom.: 6963 Cov.: 33 AF XY: 0.299 AC XY: 22236 AN XY: 74330

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.309

Alfa AF: 0.273 Hom.: 1118

Bravo AF: 0.292

Asia WGS AF: 0.455 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.59
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2468680; hg19: chr8-140521220;