8-6878467-C-T

Position:

• chr8-6878467-C-T

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 0.291 in 151,862 control chromosomes in the GnomAD database, including 6,814 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 (6814 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.44

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• 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.6878467C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GS1-24F4.2	ENST00000531701.1	n.226-6655C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44189 AN: 151744 Hom.: 6808 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.291 AC: 44214 AN: 151862 Hom.: 6814 Cov.: 31 AF XY: 0.288 AC XY: 21363 AN XY: 74210

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.335

Alfa AF: 0.240 Hom.: 976

Bravo AF: 0.297

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2741132; hg19: chr8-6735989;