rs6999780

Positions:

• chr8-66179841-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.159 in 152,188 control chromosomes in the GnomAD database, including 3,152 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 0.16 (3152 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.66179841G>A		intergenic_region
LOC112268029	XR_002956713.2	n.*45C>T		downstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24192 AN: 152070 Hom.: 3144 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.0883

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0334

Gnomad FIN AF: 0.0960

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0935

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.159 AC: 24241 AN: 152188 Hom.: 3152 Cov.: 32 AF XY: 0.156 AC XY: 11591 AN XY: 74398

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.0880

Gnomad4 ASJ AF: 0.0522

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0336

Gnomad4 FIN AF: 0.0960

Gnomad4 NFE AF: 0.0935

Gnomad4 OTH AF: 0.127

Alfa AF: 0.0983 Hom.: 1007

Bravo AF: 0.166

Asia WGS AF: 0.0450 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	14
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6999780; hg19: chr8-67092076;