rs9405098

Variant names:

• chr6-32411959-G-A
• rs9405098

Your query was ambiguous. Multiple possible variants found:

• chr6-32411959-G-A
• chr6-32411959-G-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 0.0424 in 152,182 control chromosomes in the GnomAD database, including 276 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 0.042 (276 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.2 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: 0.0424 AC: 6444 AN: 152062 Hom.: 275 Cov.: 32

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0280

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0184

Gnomad OTH AF: 0.0527

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

GnomAD4 genome AF: 0.0424 AC: 6447 AN: 152182 Hom.: 276 Cov.: 32 AF XY: 0.0457 AC XY: 3397 AN XY: 74406

Gnomad4 AFR AF: 0.0533

Gnomad4 AMR AF: 0.0280

Gnomad4 ASJ AF: 0.0652

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.0352

Gnomad4 NFE AF: 0.0184

Gnomad4 OTH AF: 0.0522

Alfa AF: 0.0205 Hom.: 31

Bravo AF: 0.0397

Asia WGS AF: 0.161 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9405098; hg19: chr6-32379736;