rs9481083

chr6-110506679-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 0.272 in 152,080 control chromosomes in the GnomAD database, including 6,357 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 0.27 (6357 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 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: 0.272 AC: 41342 AN: 151962 Hom.: 6345 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.272 AC: 41379 AN: 152080 Hom.: 6357 Cov.: 32 AF XY: 0.263 AC XY: 19531 AN XY: 74330

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.286

Alfa AF: 0.260 Hom.: 3813

Bravo AF: 0.286

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.44
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: rs9481083; hg19: chr6-110827882;