rs9405890

Variant names:

• chr6-6012488-T-C
• rs9405890

Your query was ambiguous. Multiple possible variants found:

• chr6-6012488-T-C
• chr6-6012488-T-G

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 0.355 in 152,086 control chromosomes in the GnomAD database, including 10,396 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 0.36 (10396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53994 AN: 151968 Hom.: 10384 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.355 AC: 54032 AN: 152086 Hom.: 10396 Cov.: 32 AF XY: 0.352 AC XY: 26164 AN XY: 74346

African (AFR) AF: 0.504 AC: 20879 AN: 41434

American (AMR) AF: 0.313 AC: 4782 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 965 AN: 3470

East Asian (EAS) AF: 0.283 AC: 1465 AN: 5182

South Asian (SAS) AF: 0.331 AC: 1593 AN: 4816

European-Finnish (FIN) AF: 0.289 AC: 3052 AN: 10574

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20109 AN: 67998

Other (OTH) AF: 0.349 AC: 738 AN: 2112

Alfa AF: 0.307 Hom.: 1617

Bravo AF: 0.363

Asia WGS AF: 0.327 AC: 1135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.4
DANN	Benign	0.78
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs9405890; hg19: chr6-6012721;