rs9468898

Variant names:

• chr6-31214606-A-G
• rs9468898

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0602 AC: 2500 AN: 41556

American (AMR) AF: 0.0315 AC: 482 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0225 AC: 78 AN: 3472

East Asian (EAS) AF: 0.0865 AC: 448 AN: 5180

South Asian (SAS) AF: 0.115 AC: 557 AN: 4824

European-Finnish (FIN) AF: 0.0153 AC: 163 AN: 10622

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0266 AC: 1812 AN: 68024

Other (OTH) AF: 0.0383 AC: 81 AN: 2114

Alfa AF: 0.0302 Hom.: 192

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
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs9468898; hg19: chr6-31182383;