rs7006609

chr8-83793001-A-Cchr8-83793001-A-Gchr8-83793001-A-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 0.376 in 151,636 control chromosomes in the GnomAD database, including 10,986 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 0.38 (10986 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 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

Frequencies

GnomAD3 genomes AF: 0.376 AC: 56906 AN: 151520 Hom.: 10983 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.376 AC: 56941 AN: 151636 Hom.: 10986 Cov.: 32 AF XY: 0.377 AC XY: 27966 AN XY: 74106

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.392

Alfa AF: 0.310 Hom.: 1231

Bravo AF: 0.367

Asia WGS AF: 0.382 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.31
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7006609; hg19: chr8-84705236;