9-131575806-T-C

Variant names:

• chr9-131575806-T-C
• rs943852

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 0.869 in 152,266 control chromosomes in the GnomAD database, including 57,667 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 0.87 (57667 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.869 AC: 132204 AN: 152146 Hom.: 57608 Cov.: 34

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.834

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.869 AC: 132323 AN: 152266 Hom.: 57667 Cov.: 34 AF XY: 0.869 AC XY: 64719 AN XY: 74436

African (AFR) AF: 0.938 AC: 39018 AN: 41576

American (AMR) AF: 0.852 AC: 13031 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2850 AN: 3472

East Asian (EAS) AF: 0.795 AC: 4111 AN: 5170

South Asian (SAS) AF: 0.823 AC: 3972 AN: 4824

European-Finnish (FIN) AF: 0.881 AC: 9349 AN: 10606

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57152 AN: 67996

Other (OTH) AF: 0.859 AC: 1815 AN: 2114

Alfa AF: 0.847 Hom.: 27313

Bravo AF: 0.869

Asia WGS AF: 0.839 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.44
DANN	Benign	0.26
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs943852; hg19: chr9-134451193;