rs1331504

Variant names:

• chr9-90643546-G-C
• rs1331504

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0538 in 152,300 control chromosomes in the GnomAD database, including 300 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 0.054 (300 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.20
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0941 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: 0.0539 AC: 8207 AN: 152182 Hom.: 302 Cov.: 33

Gnomad AFR AF: 0.0146

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0557

Gnomad ASJ AF: 0.0884

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0446

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0772

Gnomad OTH AF: 0.0694

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

GnomAD4 genome AF: 0.0538 AC: 8200 AN: 152300 Hom.: 300 Cov.: 33 AF XY: 0.0539 AC XY: 4016 AN XY: 74472

African (AFR) AF: 0.0145 AC: 604 AN: 41566

American (AMR) AF: 0.0556 AC: 851 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0884 AC: 307 AN: 3472

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5188

South Asian (SAS) AF: 0.102 AC: 490 AN: 4826

European-Finnish (FIN) AF: 0.0446 AC: 474 AN: 10618

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0772 AC: 5252 AN: 68020

Other (OTH) AF: 0.0672 AC: 142 AN: 2112

Alfa AF: 0.0554 Hom.: 32

Bravo AF: 0.0512

Asia WGS AF: 0.0480 AC: 168 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	14
DANN	Benign	0.73
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs1331504; hg19: chr9-93405828;