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. The variant received -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
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0533 AC: 2213 AN: 41506

American (AMR) AF: 0.0280 AC: 428 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0652 AC: 226 AN: 3466

East Asian (EAS) AF: 0.210 AC: 1084 AN: 5162

South Asian (SAS) AF: 0.155 AC: 745 AN: 4818

European-Finnish (FIN) AF: 0.0352 AC: 373 AN: 10606

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0184 AC: 1250 AN: 68014

Other (OTH) AF: 0.0522 AC: 110 AN: 2108

Alfa AF: 0.0290 Hom.: 360

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs9405098; hg19: chr6-32379736;