rs9380006

Positions:

• chr6-27688720-A-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 0.256 in 151,652 control chromosomes in the GnomAD database, including 5,898 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 0.26 (5898 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 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: 0.255 AC: 38714 AN: 151532 Hom.: 5887 Cov.: 30

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.256 AC: 38772 AN: 151652 Hom.: 5898 Cov.: 30 AF XY: 0.260 AC XY: 19277 AN XY: 74104

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.223

Alfa AF: 0.181 Hom.: 3180

Bravo AF: 0.263

Asia WGS AF: 0.318 AC: 1103 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9380006; hg19: chr6-27656499;