rs7000234

Positions:

• chr8-80624879-G-A
• chr8-80624879-G-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 0.0992 in 152,124 control chromosomes in the GnomAD database, including 1,082 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 0.099 (1082 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.80624879G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0989 AC: 15037 AN: 152006 Hom.: 1069 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.0648

Gnomad ASJ AF: 0.0799

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0611

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0664

Gnomad OTH AF: 0.0982

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

GnomAD4 genome AF: 0.0992 AC: 15084 AN: 152124 Hom.: 1082 Cov.: 32 AF XY: 0.0967 AC XY: 7193 AN XY: 74380

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.0645

Gnomad4 ASJ AF: 0.0799

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0175

Gnomad4 FIN AF: 0.0611

Gnomad4 NFE AF: 0.0663

Gnomad4 OTH AF: 0.0976

Alfa AF: 0.0708 Hom.: 233

Bravo AF: 0.103

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7000234; hg19: chr8-81537114;