chr8-6878491-G-C

Position:

• chr8-6878491-G-C

Variant summary

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

The variant allele was found at a frequency of 0.319 in 151,740 control chromosomes in the GnomAD database, including 7,918 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 0.32 (7918 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.6878491G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GS1-24F4.2	ENST00000531701.1	n.226-6631G>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48345 AN: 151622 Hom.: 7909 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.319 AC: 48377 AN: 151740 Hom.: 7918 Cov.: 31 AF XY: 0.316 AC XY: 23408 AN XY: 74148

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.353

Alfa AF: 0.163 Hom.: 313

Bravo AF: 0.326

Asia WGS AF: 0.413 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.96
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2702876; hg19: chr8-6736013;