rs9468898

chr6-31214606-A-G

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 0.0404 in 152,294 control chromosomes in the GnomAD database, including 190 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 0.040 (190 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.108 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: 0.0404 AC: 6147 AN: 152176 Hom.: 189 Cov.: 32

Gnomad AFR AF: 0.0600

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0316

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.0867

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0153

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0266

Gnomad OTH AF: 0.0387

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

GnomAD4 genome AF: 0.0404 AC: 6156 AN: 152294 Hom.: 190 Cov.: 32 AF XY: 0.0412 AC XY: 3069 AN XY: 74462

Gnomad4 AFR AF: 0.0602

Gnomad4 AMR AF: 0.0315

Gnomad4 ASJ AF: 0.0225

Gnomad4 EAS AF: 0.0865

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0153

Gnomad4 NFE AF: 0.0266

Gnomad4 OTH AF: 0.0383

Alfa AF: 0.0276 Hom.: 37

Bravo AF: 0.0419

Asia WGS AF: 0.0950 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.8
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9468898; hg19: chr6-31182383;